diff --git a/doc/Makefile b/doc/Makefile
index 79558674d75ccf99ba7ccfb29ebe4966b0356c7c..e272fc253e029d3134e47d4655903b971902abf9 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -22,7 +22,7 @@ endif
SOURCES=$(wildcard src/*.txt)
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
-.PHONY: help clean-all clean epub html pdf old venv spelling
+.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
# ------------------------------------------
@@ -36,6 +36,7 @@ help:
@echo " clean remove all intermediate RST files"
@echo " clean-all reset the entire build environment"
@echo " txt2html build txt2html tool"
+ @echo " anchor_check scan for duplicate anchor labels"
# ------------------------------------------
@@ -54,6 +55,9 @@ html: $(OBJECTS)
. $(VENV)/bin/activate ;\
cp -r src/* $(RSTDIR)/ ;\
sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+ echo "############################################" ;\
+ doc_anchor_check src/*.txt ;\
+ echo "############################################" ;\
deactivate ;\
)
-rm html/searchindex.js
@@ -127,6 +131,13 @@ fetch:
txt2html: utils/txt2html/txt2html.exe
+anchor_check : $(TXT2RST)
+ @(\
+ . $(VENV)/bin/activate ;\
+ doc_anchor_check src/*.txt ;\
+ deactivate ;\
+ )
+
# ------------------------------------------
utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
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)
diff --git a/doc/utils/converters/lammpsdoc/doc_anchor_check.py b/doc/utils/converters/lammpsdoc/doc_anchor_check.py
new file mode 100755
index 0000000000000000000000000000000000000000..a072ab1a68c8484490640854e758569194c35716
--- /dev/null
+++ b/doc/utils/converters/lammpsdoc/doc_anchor_check.py
@@ -0,0 +1,60 @@
+#! /usr/bin/env python3
+# LAMMPS Documentation Utilities
+#
+# Scan for duplicate anchor labels in documentation files
+#
+# Copyright (C) 2017 Richard Berger
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+import re
+import sys
+import argparse
+
+def main():
+ parser = argparse.ArgumentParser(description='scan for duplicate anchor labels in documentation files')
+ parser.add_argument('files', metavar='file', nargs='+', help='one or more files to scan')
+ parsed_args = parser.parse_args()
+
+ anchor_pattern = re.compile(r'^:link\(([^,\)]*)\)')
+ anchors = {}
+
+ for filename in parsed_args.files:
+ with open(filename, 'rt') as f:
+ for line_number, line in enumerate(f):
+ m = anchor_pattern.match(line)
+ if m:
+ label = m.group(1)
+ if label in anchors:
+ anchors[label].append((filename, line_number+1))
+ else:
+ anchors[label] = [(filename, line_number+1)]
+
+ count = 0
+
+ for label in sorted(anchors.keys()):
+ if len(anchors[label]) > 1:
+ print(label)
+ count += 1
+ for filename, line_number in anchors[label]:
+ print(" - %s:%d" % (filename, line_number))
+
+
+ if count > 0:
+ print("Found %d anchor label errors." % count)
+ sys.exit(1)
+ else:
+ print("No anchor label errors.")
+
+if __name__ == "__main__":
+ main()
diff --git a/doc/utils/converters/setup.py b/doc/utils/converters/setup.py
index b8a6a1a78ff582a5a6e902926aa59851acc9940b..f4656a7f697cc6e0dd7235ac873b2201a0d299d2 100644
--- a/doc/utils/converters/setup.py
+++ b/doc/utils/converters/setup.py
@@ -12,6 +12,7 @@ setup(name='LAMMPS Documentation Utilities',
tests_require=['nose'],
entry_points = {
"console_scripts": ['txt2html = lammpsdoc.txt2html:main',
- 'txt2rst = lammpsdoc.txt2rst:main']
+ 'txt2rst = lammpsdoc.txt2rst:main',
+ 'doc_anchor_check = lammpsdoc.doc_anchor_check:main ']
},
)