doc page sync with SVN

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 "  html       create HTML doc pages in html dir"
-	@echo "  pdf        to make Manual.pdf"
+	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
-	@echo "  txt2html   to build txt2html tool"
+	@echo "  old        create old-style HTML doc pages in old dir"
-	@echo "  clean      to remove all generated RST files"
+	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
-	@echo "  clean-all  to reset the entire build environment"
+	@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 $$s ../lammps.book || \
+			do grep -q $$s lammps.book || \
-			echo doc file $$s missing in lammps.book; done; \
+			echo doc file $$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 $@ $<
 

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.

doc/README.md

@@ -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.

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
 

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

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),
+  xvarstr(NULL), yvarstr(NULL), zvarstr(NULL), vxvarstr(NULL), 
-  xoriginal(NULL), toriginal(NULL), qoriginal(NULL), displace(NULL), velocity(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");
 

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");
 

src/version.h

@@ -1 +1 @@
-#define LAMMPS_VERSION "20 Sep 2016"
+#define LAMMPS_VERSION "22 Sep 2016"