Update to oxDNA2 (604afebf) · Commits · 郑智淋 / lammps

doc/Makefile

+15 −3

Original line number	Diff line number	Diff line
		@@ -6,6 +6,7 @@ BUILDDIR = /tmp/lammps-docs-$(SHA1)
		RSTDIR = $(BUILDDIR)/rst
		VENV = $(BUILDDIR)/docenv
		TXT2RST = $(VENV)/bin/txt2rst
		ANCHORCHECK = $(VENV)/bin/doc_anchor_check

		PYTHON = $(shell which python3)
		HAS_PYTHON3 = NO
		@@ -22,7 +23,7 @@ endif
		SOURCES=$(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 +37,7 @@ 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"

		# ------------------------------------------

		@@ -49,11 +51,14 @@ clean:
		clean-spelling:
		rm -rf spelling

		html: $(OBJECTS)
		html: $(OBJECTS) $(ANCHORCHECK)
		@(\
		. $(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 +132,13 @@ fetch:

		txt2html: utils/txt2html/txt2html.exe

		anchor_check : $(ANCHORCHECK)
		@(\
		. $(VENV)/bin/activate ;\
		doc_anchor_check src/*.txt ;\
		deactivate ;\
		)

		# ------------------------------------------

		utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
		@@ -151,7 +163,7 @@ $(VENV):
		deactivate;\
		)

		$(TXT2RST): $(VENV)
		$(TXT2RST) $(ANCHORCHECK): $(VENV)
		@( \
		. $(VENV)/bin/activate; \
		(cd utils/converters;\

doc/src/Eqs/pair_momb.jpg

0 → 100644

+17.4 KiB

Loading image diff...

doc/src/Eqs/pair_momb.tex

0 → 100644

+13 −0

Original line number	Diff line number	Diff line
		\documentclass[12pt,fleqn]{article}
		\usepackage{amsmath}
		\thispagestyle{empty}

		\begin{document}

		\setlength{\jot}{2ex}
		\begin{gather*}
		E = D_0 [\exp^{-2 \alpha (r-r_0)} - 2\exp^{-\alpha (r-r_0)}] - s_6 \frac{C_6}{r^6} f_{damp}(r,R_r) \\
		f_{damp}(r,R_r) = \frac{1}{1 + \exp^{-d(r/R_r - 1)}}
		\end{gather*}

		\end{document}
		No newline at end of file

doc/src/Manual.txt

+4 −4

Original line number	Diff line number	Diff line
		<!-- HTML_ONLY -->
		<HEAD>
		<TITLE>LAMMPS Users Manual</TITLE>
		<META NAME="docnumber" CONTENT="10 Mar 2017 version">
		<META NAME="docnumber" CONTENT="24 Mar 2017 version">
		<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
		<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
		</HEAD>
		@@ -21,7 +21,7 @@
		<H1></H1>

		LAMMPS Documentation :c,h3
		10 Mar 2017 version :c,h4
		24 Mar 2017 version :c,h4

		Version info: :h4

		@@ -39,7 +39,7 @@ directory name created when you unpack a tarball, and at the top of
		the first page of the manual (this page).

		If you browse the HTML doc pages on the LAMMPS WWW site, they always
		describe the most current version of LAMMPS. :ulb,l
		describe the most current [development] version of LAMMPS. :ulb,l

		If you browse the HTML doc pages included in your tarball, they
		describe the version you have. :l
		@@ -67,7 +67,7 @@ Labs and Temple University:

		"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l
		Aidan Thompson, athomps at sandia.gov :l
		Stan Moore, stamoore at sandia.gov :l
		Stan Moore, stamoor at sandia.gov :l
		"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
		:ule

doc/src/Section_commands.txt

+6 −1

Original line number	Diff line number	Diff line
		@@ -687,6 +687,7 @@ package"_Section_start.html#start_3.
		"eos/cv"_fix_eos_cv.html,
		"eos/table"_fix_eos_table.html,
		"eos/table/rx"_fix_eos_table_rx.html,
		"filter/corotate"_fix_filter_corotate.html,
		"flow/gauss"_fix_flow_gauss.html,
		"gle"_fix_gle.html,
		"grem"_fix_grem.html,
		@@ -939,6 +940,8 @@ KOKKOS, o = USER-OMP, t = OPT.
		"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
		"lj/charmm/coul/long (giko)"_pair_charmm.html,
		"lj/charmm/coul/msm"_pair_charmm.html,
		"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
		"lj/charmmfsw/coul/long"_pair_charmm.html,
		"lj/class2 (gko)"_pair_class2.html,
		"lj/class2/coul/cut (ko)"_pair_class2.html,
		"lj/class2/coul/long (gko)"_pair_class2.html,
		@@ -1034,6 +1037,7 @@ package"_Section_start.html#start_3.
		"meam/spline (o)"_pair_meam_spline.html,
		"meam/sw/spline"_pair_meam_sw_spline.html,
		"mgpt"_pair_mgpt.html,
		"momb"_pair_momb.html,
		"morse/smooth/linear"_pair_morse.html,
		"morse/soft"_pair_morse.html,
		"multi/lucy"_pair_multi_lucy.html,
		@@ -1146,6 +1150,7 @@ USER-OMP, t = OPT.
		"zero"_dihedral_zero.html,
		"hybrid"_dihedral_hybrid.html,
		"charmm (ko)"_dihedral_charmm.html,
		"charmmfsh"_dihedral_charmm.html,
		"class2 (ko)"_dihedral_class2.html,
		"harmonic (io)"_dihedral_harmonic.html,
		"helix (o)"_dihedral_helix.html,

Admin message