diff --git a/doc/Developer.pdf b/doc/Developer.pdf deleted file mode 100644 index 55b5015e49..0000000000 Binary files a/doc/Developer.pdf and /dev/null differ diff --git a/doc/Makefile b/doc/Makefile index 52ed2d0d73..256dcd51c6 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 ' where 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 0f5f3497dc..0000000000 Binary files a/doc/Manual.pdf and /dev/null differ diff --git a/doc/README b/doc/README new file mode 100644 index 0000000000..686a1802a4 --- /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 b843b7eabe..0000000000 --- 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 3e822bd968..b276794a51 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

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 f28bb48b56..620eee483d 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 3c07977382..d3c4b12e3d 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 e2ce97db43..01ba81e554 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 c55689c662..c6df1e4175 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "20 Sep 2016" +#define LAMMPS_VERSION "22 Sep 2016"