forked from lijiext/lammps
Merge pull request #420 from rbberger/doc_anchor_check
Add utility to detect duplicate anchors in docs
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sjplimp
GitHub
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13
doc/Makefile
13
doc/Makefile
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@ -22,7 +22,7 @@ endif
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SOURCES=$(wildcard src/*.txt)
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OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
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.PHONY: help clean-all clean epub html pdf old venv spelling
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.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
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# ------------------------------------------
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@ -36,6 +36,7 @@ help:
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@echo " clean remove all intermediate RST files"
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@echo " clean-all reset the entire build environment"
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@echo " txt2html build txt2html tool"
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@echo " anchor_check scan for duplicate anchor labels"
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# ------------------------------------------
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@ -54,6 +55,9 @@ html: $(OBJECTS)
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. $(VENV)/bin/activate ;\
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cp -r src/* $(RSTDIR)/ ;\
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sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
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echo "############################################" ;\
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doc_anchor_check src/*.txt ;\
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echo "############################################" ;\
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deactivate ;\
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)
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-rm html/searchindex.js
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@ -127,6 +131,13 @@ fetch:
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txt2html: utils/txt2html/txt2html.exe
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anchor_check : $(TXT2RST)
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@(\
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. $(VENV)/bin/activate ;\
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doc_anchor_check src/*.txt ;\
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deactivate ;\
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)
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# ------------------------------------------
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utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
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@ -36,7 +36,7 @@ uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html
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command should be used to perform charge equilibration with the "COMB
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potential"_pair_comb.html. For more technical details about the
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charge equilibration performed by fix qeq/reax, see the
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"(Aktulga)"_#Aktulga paper.
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"(Aktulga)"_#qeq-Aktulga paper.
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The QEq method minimizes the electrostatic energy of the system by
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adjusting the partial charge on individual atoms based on interactions
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@ -119,6 +119,6 @@ be used for periodic cell dimensions less than 10 angstroms.
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:link(Nakano)
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[(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997).
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:link(Aktulga)
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(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
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:link(qeq-Aktulga)
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[(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
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245-259 (2012).
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@ -52,7 +52,7 @@ to Stillinger-Weber potential ("SW"_#SW) if we set
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:c,image(Eqs/polymorphic4.jpg)
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The potential reduces to Tersoff types of potential
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("Tersoff"_#Tersoff or "Albe"_#Albe) if we set
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("Tersoff"_#Tersoff or "Albe"_#poly-Albe) if we set
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:c,image(Eqs/polymorphic5.jpg)
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:c,image(Eqs/polymorphic6.jpg)
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@ -63,7 +63,7 @@ The potential reduces to Rockett-Tersoff ("Wang"_#Wang) type if we set
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:c,image(Eqs/polymorphic6.jpg)
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:c,image(Eqs/polymorphic8.jpg)
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The potential becomes embedded atom method ("Daw"_#Daw) if we set
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The potential becomes embedded atom method ("Daw"_#poly-Daw) if we set
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:c,image(Eqs/polymorphic9.jpg)
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@ -218,12 +218,12 @@ F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015).
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:link(Tersoff)
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[(Tersoff)] J. Tersoff, Phys. Rev. B, 39, 5566 (1989).
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:link(Albe)
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:link(poly-Albe)
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[(Albe)] K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B,
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66, 035205 (2002).
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:link(Wang)
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[(Wang)] J. Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991).
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:link(Daw)
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:link(poly-Daw)
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[(Daw)] M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).
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@ -23,9 +23,9 @@ pair_coeff * * SiC.tersoff.zbl Si C Si :pre
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[Description:]
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The {tersoff/zbl} style computes a 3-body Tersoff potential
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"(Tersoff_1)"_#Tersoff_1 with a close-separation pairwise modification
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"(Tersoff_1)"_#zbl-Tersoff_1 with a close-separation pairwise modification
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based on a Coulomb potential and the Ziegler-Biersack-Littmark
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universal screening function "(ZBL)"_#ZBL, giving the energy E of a
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universal screening function "(ZBL)"_#zbl-ZBL, giving the energy E of a
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system of atoms as
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:c,image(Eqs/pair_tersoff_zbl.jpg)
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@ -146,16 +146,16 @@ be set to 0.0 if desired.
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Note that the twobody parameters in entries such as SiCC and CSiSi
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are often the same, due to the common use of symmetric mixing rules,
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but this is not always the case. For example, the beta and n parameters in
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Tersoff_2 "(Tersoff_2)"_#Tersoff_2 are not symmetric.
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Tersoff_2 "(Tersoff_2)"_#zbl-Tersoff_2 are not symmetric.
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We chose the above form so as to enable users to define all commonly
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used variants of the Tersoff portion of the potential. In particular,
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our form reduces to the original Tersoff form when m = 3 and gamma =
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1, while it reduces to the form of "Albe et al."_#Albe when beta = 1
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1, while it reduces to the form of "Albe et al."_#zbl-Albe when beta = 1
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and m = 1. Note that in the current Tersoff implementation in LAMMPS,
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m must be specified as either 3 or 1. Tersoff used a slightly
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different but equivalent form for alloys, which we will refer to as
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Tersoff_2 potential "(Tersoff_2)"_#Tersoff_2.
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Tersoff_2 potential "(Tersoff_2)"_#zbl-Tersoff_2.
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LAMMPS parameter values for Tersoff_2 can be obtained as follows:
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gamma = omega_ijk, lambda3 = 0 and the value of
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@ -253,16 +253,16 @@ units.
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:line
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:link(Tersoff_1)
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:link(zbl-Tersoff_1)
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[(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988).
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:link(ZBL)
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:link(zbl-ZBL)
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[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges
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of Ions in Matter' Vol 1, 1985, Pergamon Press.
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:link(Albe)
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:link(zbl-Albe)
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[(Albe)] J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.:
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Condens. Matter, 15, 5649(2003).
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:link(Tersoff_2)
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:link(zbl-Tersoff_2)
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[(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
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@ -0,0 +1,60 @@
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#! /usr/bin/env python3
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# LAMMPS Documentation Utilities
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#
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# Scan for duplicate anchor labels in documentation files
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#
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# Copyright (C) 2017 Richard Berger
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with this program. If not, see <http://www.gnu.org/licenses/>.
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import re
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import sys
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import argparse
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def main():
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parser = argparse.ArgumentParser(description='scan for duplicate anchor labels in documentation files')
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parser.add_argument('files', metavar='file', nargs='+', help='one or more files to scan')
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parsed_args = parser.parse_args()
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anchor_pattern = re.compile(r'^:link\(([^,\)]*)\)')
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anchors = {}
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for filename in parsed_args.files:
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with open(filename, 'rt') as f:
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for line_number, line in enumerate(f):
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m = anchor_pattern.match(line)
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if m:
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label = m.group(1)
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if label in anchors:
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anchors[label].append((filename, line_number+1))
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else:
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anchors[label] = [(filename, line_number+1)]
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count = 0
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for label in sorted(anchors.keys()):
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if len(anchors[label]) > 1:
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print(label)
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count += 1
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for filename, line_number in anchors[label]:
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print(" - %s:%d" % (filename, line_number))
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if count > 0:
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print("Found %d anchor label errors." % count)
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sys.exit(1)
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else:
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print("No anchor label errors.")
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if __name__ == "__main__":
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main()
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@ -12,6 +12,7 @@ setup(name='LAMMPS Documentation Utilities',
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tests_require=['nose'],
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entry_points = {
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"console_scripts": ['txt2html = lammpsdoc.txt2html:main',
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'txt2rst = lammpsdoc.txt2rst:main']
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'txt2rst = lammpsdoc.txt2rst:main',
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'doc_anchor_check = lammpsdoc.doc_anchor_check:main ']
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},
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)
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