diff --git a/doc/Developer.pdf b/doc/Developer.pdf
deleted file mode 100644
index 55b5015e49ebaf8e791be383349f6d5023e48f8a..0000000000000000000000000000000000000000
Binary files a/doc/Developer.pdf and /dev/null differ
diff --git a/doc/Makefile b/doc/Makefile
index 52ed2d0d73fca104446db1830c4a8caa1602e860..256dcd51c63940fe05a5fd52cd84f0a6ade542aa 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -1,4 +1,6 @@
# Makefile for LAMMPS documentation
+
+SHELL = /bin/bash
SHA1 = $(shell echo $USER-$PWD | python utils/sha1sum.py)
BUILDDIR = /tmp/lammps-docs-$(SHA1)
RSTDIR = $(BUILDDIR)/rst
@@ -18,15 +20,21 @@ endif
SOURCES=$(wildcard src/*.txt)
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
-.PHONY: help clean-all clean html pdf venv
+.PHONY: help clean-all clean html pdf old venv
+
+# ------------------------------------------
help:
@echo "Please use \`make <target>' where <target> is one of"
- @echo " html to make HTML version of documentation using Sphinx"
- @echo " pdf to make Manual.pdf"
- @echo " txt2html to build txt2html tool"
- @echo " clean to remove all generated RST files"
- @echo " clean-all to reset the entire build environment"
+ @echo " html create HTML doc pages in html dir"
+ @echo " pdf create Manual.pdf and Developer.pdf in this dir"
+ @echo " old create old-style HTML doc pages in old dir"
+ @echo " fetch fetch HTML and PDF files from LAMMPS web site"
+ @echo " clean remove all intermediate RST files"
+ @echo " clean-all reset the entire build environment"
+ @echo " txt2html build txt2html tool"
+
+# ------------------------------------------
clean-all:
rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
@@ -34,8 +42,6 @@ clean-all:
clean:
rm -rf $(RSTDIR)
-txt2html: utils/txt2html/txt2html.exe
-
html: $(OBJECTS)
@(\
. $(VENV)/bin/activate ;\
@@ -44,20 +50,53 @@ html: $(OBJECTS)
deactivate ;\
)
-rm html/searchindex.js
- -rm -rf html/_sources
+ @rm -rf html/_sources
+ @rm -rf html/PDF
+ @rm -rf html/USER
+ @cp -r src/PDF html/PDF
+ @cp -r src/USER html/USER
+ @rm -rf html/PDF/.[sg]*
+ @rm -rf html/USER/.[sg]*
+ @rm -rf html/USER/*/.[sg]*
+ @rm -rf html/USER/*/*.[sg]*
@echo "Build finished. The HTML pages are in doc/html."
pdf: utils/txt2html/txt2html.exe
@(\
cd src; \
../utils/txt2html/txt2html.exe -b *.txt; \
- htmldoc --batch ../lammps.book; \
+ htmldoc --batch lammps.book; \
for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
- do grep -q $$s ../lammps.book || \
- echo doc file $$s missing in lammps.book; done; \
+ do grep -q $$s lammps.book || \
+ echo doc file $$s missing in src/lammps.book; done; \
rm *.html; \
+ cd Developer; \
+ pdflatex developer; \
+ pdflatex developer; \
+ mv developer.pdf ../../Developer.pdf; \
)
+old: utils/txt2html/txt2html.exe
+ @rm -rf old
+ @mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
+ @cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
+ mv *.html ../old; \
+ cp Eqs/*.jpg ../old/Eqs; \
+ cp JPG/* ../old/JPG; \
+ cp PDF/* ../old/PDF;
+
+fetch:
+ @rm -rf html_www Manual_www.pdf Developer_www.pdf
+ @curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
+ @curl -s -o Developer_www.pdf http://lammps.sandia.gov/doc/Developer.pdf
+ @curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
+ @tar xzf lammps-doc.tar.gz
+ @rm -f lammps-doc.tar.gz
+
+txt2html: utils/txt2html/txt2html.exe
+
+# ------------------------------------------
+
utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
g++ -O -Wall -o $@ $<
diff --git a/doc/Manual.pdf b/doc/Manual.pdf
deleted file mode 100644
index 0f5f3497dc657b57929c6be81db34366ace7d0e6..0000000000000000000000000000000000000000
Binary files a/doc/Manual.pdf and /dev/null differ
diff --git a/doc/README b/doc/README
new file mode 100644
index 0000000000000000000000000000000000000000..686a1802a4fb8e47ff07a52eb92098c581371dc8
--- /dev/null
+++ b/doc/README
@@ -0,0 +1,53 @@
+Generation of LAMMPS Documentation
+
+The generation of all documentation is managed by the Makefile in this
+dir.
+
+----------------
+
+Options:
+
+make html # generate HTML in html dir using Sphinx
+make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
+ # in this dir via htmldoc and pdflatex
+make old # generate old-style HTML pages in old dir via txt2html
+make fetch # fetch HTML doc pages and 2 PDF files from web site
+ # as a tarball and unpack into html dir and 2 PDFs
+make clean # remove intermediate RST files created by HTML build
+make clean-all # remove entire build folder and any cached data
+
+----------------
+
+Installing prerequisites for HTML build
+
+To run the HTML documention build toolchain, Python 3 and virtualenv
+have to be installed. Here are instructions for common setups:
+
+# Ubuntu
+
+sudo apt-get install python-virtualenv
+
+# Fedora (up to version 21)
+# Red Hat Enterprise Linux or CentOS (up to version 7.x)
+
+sudo yum install python3-virtualenv
+
+# Fedora (since version 22)
+
+sudo dnf install python3-virtualenv
+
+# MacOS X
+
+## Python 3
+
+Download the latest Python 3 MacOS X package from
+https://www.python.org and install it. This will install both Python
+3 and pip3.
+
+## virtualenv
+
+Once Python 3 is installed, open a Terminal and type
+
+pip3 install virtualenv
+
+This will install virtualenv from the Python Package Index.
diff --git a/doc/README.md b/doc/README.md
deleted file mode 100644
index b843b7eabe85e1ae5c9bbf2f0ad446a26e997509..0000000000000000000000000000000000000000
--- a/doc/README.md
+++ /dev/null
@@ -1,48 +0,0 @@
-# Generation of LAMMPS Documentation
-
-The generation of all the documentation is managed by the Makefile inside the
-`doc/` folder.
-
-## Usage:
-
-```bash
-make html # generate HTML using Sphinx
-make pdf # generate PDF using htmldoc
-make clean # remove generated RST files
-make clean-all # remove entire build folder and any cached data
-```
-
-## Installing prerequisites
-
-To run the documention build toolchain, Python 3 and virtualenv have
-to be installed. Here are instructions for common setups:
-
-### Ubuntu
-
-```bash
-sudo apt-get install python-virtualenv
-```
-
-### Fedora (up to version 21), Red Hat Enterprise Linux or CentOS (up to version 7.x)
-
-```bash
-sudo yum install python3-virtualenv
-```
-
-### Fedora (since version 22)
-
-```bash
-sudo dnf install python3-virtualenv
-```
-
-### MacOS X
-
-## Python 3
-
-Download the latest Python 3 MacOS X package from https://www.python.org and install it.
-This will install both Python 3 and pip3.
-
-## virtualenv
-
-Once Python 3 is installed, open a Terminal and type `pip3 install virtualenv`. This will
-install virtualenv from the Python Package Index.
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 3e822bd968ca1ed08f702f2b3b037c5c3fca20b1..b276794a515424fc38f439d4d30848ceff93cde2 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="20 Sep 2016 version">
+<META NAME="docnumber" CONTENT="22 Sep 2016 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
-20 Sep 2016 version :c,h4
+22 Sep 2016 version :c,h4
Version info: :h4
diff --git a/doc/lammps.book b/doc/src/lammps.book
similarity index 99%
rename from doc/lammps.book
rename to doc/src/lammps.book
index f28bb48b56b40561b0aa56750c8e5f7ff901dedb..620eee483db1b65edfad2b8641545529142a25a7 100644
--- a/doc/lammps.book
+++ b/doc/src/lammps.book
@@ -247,7 +247,6 @@ fix_smd_integrate_tlsph.html
fix_smd_integrate_ulsph.html
fix_smd_move_triangulated_surface.html
fix_smd_setvel.html
-fix_smd_tlsph_reference_configuration.html
fix_smd_wall_surface.html
fix_spring.html
fix_spring_chunk.html
@@ -262,7 +261,6 @@ fix_temp_rescale.html
fix_temp_rescale_eff.html
fix_tfmc.html
fix_thermal_conductivity.html
-fix_ti_rs.html
fix_ti_spring.html
fix_tmd.html
fix_ttm.html
diff --git a/src/fix_move.cpp b/src/fix_move.cpp
index 3c079773820c1110cf5412911161b05a9b4cc8fe..d3c4b12e3d1163a00eb90034172d4258d31841d6 100644
--- a/src/fix_move.cpp
+++ b/src/fix_move.cpp
@@ -48,8 +48,10 @@ enum{EQUAL,ATOM};
FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- xvarstr(NULL), yvarstr(NULL), zvarstr(NULL), vxvarstr(NULL), vyvarstr(NULL), vzvarstr(NULL),
- xoriginal(NULL), toriginal(NULL), qoriginal(NULL), displace(NULL), velocity(NULL)
+ xvarstr(NULL), yvarstr(NULL), zvarstr(NULL), vxvarstr(NULL),
+ vyvarstr(NULL), vzvarstr(NULL),
+ xoriginal(NULL), toriginal(NULL), qoriginal(NULL),
+ displace(NULL), velocity(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal fix move command");
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index e2ce97db43cfed0df5deb2fde1c66b7b4f581ba8..01ba81e5547c09c2dfc84418f4824e90206c3b90 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -54,7 +54,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
tstat_flag(0), pstat_flag(0),
rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL),
tcomputeflag(0), pcomputeflag(0), eta(NULL), eta_dot(NULL), eta_dotdot(NULL),
-eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL), etap_mass(NULL), mpchain(0)
+eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL),
+etap_mass(NULL), mpchain(0)
{
if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command");
diff --git a/src/version.h b/src/version.h
index c55689c662628dbecf8fb140bebe2ef64e542b23..c6df1e4175f404526a6de259ec2fa8c659187a05 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "20 Sep 2016"
+#define LAMMPS_VERSION "22 Sep 2016"