sync with GH

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15795 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Makefile

@@ -22,7 +22,7 @@ endif
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean html pdf old venv
+.PHONY: help clean-all clean epub html pdf old venv
 
 # ------------------------------------------
 
@@ -32,6 +32,7 @@ help:
 	@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 "  epub       create ePUB format manual for e-book readers"
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
@@ -63,6 +64,20 @@ html: $(OBJECTS)
 	@rm -rf html/USER/*/*.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
+epub: $(OBJECTS)
+	@mkdir -p epub
+	@rm -f LAMMPS.epub
+	@cp src/JPG/lammps-logo.png epub/
+	@(\
+		. $(VENV)/bin/activate ;\
+		cp -r src/* $(RSTDIR)/ ;\
+		sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		deactivate ;\
+	)
+	@mv  epub/LAMMPS.epub .
+	@rm -rf epub
+	@echo "Build finished. The ePUB manual file is created."
+
 pdf: utils/txt2html/txt2html.exe
 	@(\
 		cd src; \

doc/README

@@ -1,13 +1,14 @@
 LAMMPS Documentation
 
 Depending on how you obtained LAMMPS, this directory has 2 or 3
-sub-directories and optionally 2 PDF files:
+sub-directories and optionally 2 PDF files and an ePUB file:
 
 src             content files for LAMMPS documentation
 html            HTML version of the LAMMPS manual (see html/Manual.html)
 tools           tools and settings for building the documentation
 Manual.pdf      large PDF version of entire manual
 Developer.pdf   small PDF with info about how LAMMPS is structured
+LAMMPS.epub     Manual in ePUB format
 
 If you downloaded LAMMPS as a tarball from the web site, all these
 directories and files should be included.
@@ -49,6 +50,7 @@ make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
 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 epub         # generate LAMMPS.epub in ePUB format using Sphinx 
 make clean        # remove intermediate RST files created by HTML build
 make clean-all    # remove entire build folder and any cached data
 
@@ -91,3 +93,23 @@ This will install virtualenv from the Python Package Index.
 ----------------
 
 Installing prerequisites for PDF build
+
+[TBA]
+
+----------------
+
+Installing prerequisites for epub build
+
+## ePUB
+
+Same as for HTML. This uses the same tools and configuration
+files as the HTML tree.
+
+For converting the generated ePUB file to a mobi format file
+(for e-book readers like Kindle, that cannot read ePUB), you
+also need to have the 'ebook-convert' tool from the "calibre"
+software installed. http://calibre-ebook.com/
+You first create the ePUB file with 'make epub' and then do:
+
+ebook-convert LAMMPS.epub LAMMPS.mobi
+

doc/utils/sphinx-config/conf.py

@@ -276,4 +276,27 @@ texinfo_documents = [
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
 
+# -- Options for ePUB output ----------------------------------------------
+
+epub_title = 'LAMMPS Documentation - ' + get_lammps_version()
+
+epub_cover = ('lammps-logo.png', '')
+
+epub_description = """
+This is the Manual for the LAMMPS software package.
+
+LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
+Simulator and is a classical molecular dynamics simulation code
+designed to run efficiently on parallel computers.  It was developed
+at Sandia National Laboratories, a US Department of Energy facility,
+with funding from the DOE.  It is an open-source code, distributed
+freely under the terms of the GNU Public License (GPL).
+
+The primary author of the code is Steve Plimpton, who can be emailed
+at sjplimp@sandia.gov.  The LAMMPS WWW Site at lammps.sandia.gov has
+more information about the code and its uses.
+"""
+
+epub_author = 'The LAMMPS Developers'
+
 

src/MOLECULE/bond_table.cpp

@@ -585,17 +585,26 @@ double BondTable::splint(double *xa, double *ya, double *y2a, int n, double x)
 
 /* ----------------------------------------------------------------------
    calculate potential u and force f at distance x
-   insure x is between bond min/max
+   insure x is between bond min/max, exit with error if not
 ------------------------------------------------------------------------- */
 
 void BondTable::uf_lookup(int type, double x, double &u, double &f)
 {
   int itable;
   double fraction,a,b;
+  char estr[128];
 
   Table *tb = &tables[tabindex[type]];
-  x = MAX(x,tb->lo);
-  x = MIN(x,tb->hi);
+  if (x < tb->lo) {
+    sprintf(estr,"Bond length < table inner cutoff: "
+            "type %d length %g",type,x);
+    error->one(FLERR,estr);
+  }
+  if (x > tb->hi) {
+    sprintf(estr,"Bond length > table outer cutoff: "
+            "type %d length %g",type,x);
+    error->one(FLERR,estr);
+  }
 
   if (tabstyle == LINEAR) {
     itable = static_cast<int> ((x - tb->lo) * tb->invdelta);

src/create_box.cpp

@@ -159,6 +159,7 @@ void CreateBox::command(int narg, char **arg)
     } else if (strcmp(arg[iarg],"extra/special/per/atom") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
       force->special_extra = force->inumeric(FLERR,arg[iarg+1]);
+      atom->maxspecial += force->special_extra;
       iarg += 2;
     } else error->all(FLERR,"Illegal create_box command");
   }

src/molecule.cpp

@@ -595,6 +595,10 @@ void Molecule::read(int flag)
   // set maxspecial on first pass, so allocate() has a size
 
   if (bondflag && specialflag == 0) {
+    if (domain->box_exist == 0)
+      error->all(FLERR,"Cannot auto-generate special bonds before "
+                       "simulation box is defined");
+
     maxspecial = atom->maxspecial;
     if (flag) {
       special_generate();