Merge pull request #252 from akohlmey/preinstalled-vs-scm

remove the misleading "(which it is by default)" from several doc files
Merge pull request #249 from lammps/unstable
2016-11-04 10:59:06 -06:00 · 2016-11-04 10:58:55 -06:00 · 2016-11-04 10:58:42 -06:00 · 2016-11-04 10:58:14 -06:00 · 2016-11-04 10:57:43 -06:00 · 2016-11-04 10:57:20 -06:00
419 changed files with 3785 additions and 1469 deletions
--- a/doc/.gitignore
+++ b/doc/.gitignore
@ -1 +1,5 @@
 /html
+/LAMMPS.epub
+/LAMMPS.mobi
+/Manual.pdf
+/Developer.pdf
--- a/doc/Makefile
+++ b/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; \
--- a/doc/README
+++ b/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
+
--- a/doc/src/JPG/lammps-logo.png
+++ b/doc/src/JPG/lammps-logo.png
--- 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="19 Oct 2016 version">
+<META NAME="docnumber" CONTENT="27 Oct 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
-19 Oct 2016 version :c,h4
+27 Oct 2016 version :c,h4

 Version info: :h4

--- a/doc/src/PDF/colvars-refman-lammps.pdf
+++ b/doc/src/PDF/colvars-refman-lammps.pdf
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -106,7 +106,7 @@ the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
 "x".

 How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable doc page for details.
+of variable it is; see the "variable"_variable.html doc page for details.
 It can be a variable that stores multiple text strings, and return one
 of them.  The returned text string can be multiple "words" (space
 separated) which will then be interpreted as multiple arguments in the
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@ -8116,11 +8116,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd

 {Out of range atoms - cannot compute PPPM} :dt

@ -8132,11 +8132,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd

 {Out of range atoms - cannot compute PPPMDisp} :dt

@ -8148,11 +8148,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd

 {Overflow of allocated fix vector storage} :dt

--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -1864,8 +1864,8 @@ void lammps_close(void *)
 int lammps_version(void *)
 void lammps_file(void *, char *)
 char *lammps_command(void *, char *)
-char *lammps_commands_list(void *, int, char **)
-char *lammps_commands_concatenated(void *, char *)
+void lammps_commands_list(void *, int, char **)
+void lammps_commands_string(void *, char *)
 void lammps_free(void *) :pre

 The lammps_open() function is used to initialize LAMMPS, passing in a
@ -1901,51 +1901,66 @@ changes to the LAMMPS command syntax between versions. The returned
 LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
 20150902) that grows with every new LAMMPS version.

-The lammps_file(), lammps_command(), lammps_commands_list(),
-lammps_commands_concatenated() functions are used to pass one or more
-commands to LAMMPS to execute as if they were coming from an input
-script.
+The lammps_file(), lammps_command(), lammps_commands_list(), and
+lammps_commands_string() functions are used to pass one or more
+commands to LAMMPS to execute, the same as if they were coming from an
+input script.
+
+Via these functions, the calling code can read or generate a series of
+LAMMPS commands one or multiple at a time and pass it thru the library
+interface to setup a problem and then run it in stages.  The caller
+can interleave the command function calls with operations it performs,
+calls to extract information from or set information within LAMMPS, or
+calls to another code's library.

 The lammps_file() function passes the filename of an input script.
 The lammps_command() function passes a single command as a string.
-The lammps_commands_multiple() function passes multiple commands in a
-char** list.  The lammps_commands_concatentaed() function passes
-multiple commands concatenated into one long string, separated by
-newline characters.  A single command can be spread across multiple
-lines, if the last printable character of all but the last line is
-"&", the same as if the lines appeared in an input script.
+The lammps_commands_list() function passes multiple commands in a
+char** list.  In both lammps_command() and lammps_commands_list(),
+individual commands may or may not have a trailing newline.  The
+lammps_commands_string() function passes multiple commands
+concatenated into one long string, separated by newline characters.
+In both lammps_commands_list() and lammps_commands_string(), a single
+command can be spread across multiple lines, if the last printable
+character of all but the last line is "&", the same as if the lines
+appeared in an input script.

-Via these library functions, the calling code can read or generate a
-series of LAMMPS commands one or multiple at a time and pass it thru
-the library interface to setup a problem and then run it, interleaving
-the command function calls with operations performed within the
-faller, calls to extract information from LAMMPS, or calls to another
-code's library.
-
-The lammps_free() is a clean-up function to free memory that the library
-allocated previously.
+The lammps_free() function is a clean-up function to free memory that
+the library allocated previously via other function calls.  See
+comments in src/library.cpp file for which other functions need this
+clean-up.

 Library.cpp also contains these functions for extracting information
 from LAMMPS and setting value within LAMMPS.  Again, see the
-documentation in the src/library.cpp file for details:
+documentation in the src/library.cpp file for details, including
+which quantities can be queried by name:

 void *lammps_extract_global(void *, char *)
 void *lammps_extract_atom(void *, char *)
 void *lammps_extract_compute(void *, char *, int, int)
 void *lammps_extract_fix(void *, char *, int, int, int, int)
-void *lammps_extract_variable(void *, char *, char *)
+void *lammps_extract_variable(void *, char *, char *) :pre
+
 int lammps_set_variable(void *, char *, char *)
-double lammps_get_thermo(void *, char *)
+double lammps_get_thermo(void *, char *) :pre
+
 int lammps_get_natoms(void *)
 void lammps_gather_atoms(void *, double *)
 void lammps_scatter_atoms(void *, double *) :pre
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *) :pre

-These functions can extract various global or per-atom quantities from
-LAMMPS as well as values calculated by a compute, fix, or variable.
-The lammps_set_variable() function can set an existing string-style variable
-to a new value, so that subsequent LAMMPS commands can access the
-variable.  The lammps_get_thermo() function returns the current
-value of a thermo keyword.
+The extract functions return a pointer to various global or per-atom
+quantities stored in LAMMPS or to values calculated by a compute, fix,
+or variable.  The pointer returned by the extract_global() function
+can be used as a permanent reference to a value which may change.  For
+the other extract functions, the underlying storage may be reallocated
+as LAMMPS runs, so you need to re-call the function to assure a
+current pointer or returned value(s).
+
+The lammps_set_variable() function can set an existing string-style
+variable to a new string value, so that subsequent LAMMPS commands can
+access the variable.  The lammps_get_thermo() function returns the
+current value of a thermo keyword as a double.

 The lammps_get_natoms() function returns the total number of atoms in
 the system and can be used by the caller to allocate space for the
@ -1956,15 +1971,22 @@ returns a full list to each calling processor.  The scatter function
 does the inverse.  It distributes the same kinds of values, 
 passed by the caller, to each atom owned by individual processors.

+The lammps_create_atoms() function takes a list of N atoms as input
+with atom types and coords (required), an optionally atom IDs and
+velocities.  It uses the coords of each atom to assign it as a new
+atom to the processor that owns it.  Additional properties for the new
+atoms can be assigned via the lammps_scatter_atoms() or
+lammps_extract_atom() functions.
+
 The examples/COUPLE and python directories have example C++ and C and
 Python codes which show how a driver code can link to LAMMPS as a
 library, run LAMMPS on a subset of processors, grab data from LAMMPS,
 change it, and put it back into LAMMPS.

-NOTE: You can write your own additional functions as needed to define
+NOTE: You can write code for additional functions as needed to define
 how your code talks to LAMMPS and add them to src/library.cpp and
 src/library.h, as well as to the "Python
-interface"_Section_python.html.  The routines you add can access or
+interface"_Section_python.html.  The added functions can access or
 change any LAMMPS data you wish.

 :line
@ -2707,7 +2729,7 @@ production runs and is only required during equilibration. This way one
 is consistent with literature (based on the code packages DL_POLY or
 GULP for instance).

-The mentioned energy transfer will typically lead to a a small drift
+The mentioned energy transfer will typically lead to a small drift
 in total energy over time.  This internal energy can be monitored
 using the "compute chunk/atom"_compute_chunk_atom.html and "compute
 temp/chunk"_compute_temp_chunk.html commands.  The internal kinetic
@ -2808,7 +2830,7 @@ temp/drude"_compute_temp_drude.html. This requires also to use the
 command {comm_modify vel yes}.

 Short-range damping of the induced dipole interactions can be achieved
-using Thole functions through the the "pair style
+using Thole functions through the "pair style
 thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
 with a Coulomb pair style. It may be useful to use {coul/long/cs} or
 similar from the CORESHELL package if the core and Drude particle come
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -1153,6 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
 "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@ -1598,6 +1599,29 @@ The person who created this package is Axel Kohlmeyer at Temple U

 :line

+USER-NC-DUMP package :link(USER-NC-DUMP),h5
+
+Contents: Dump styles for writing NetCDF format files.  NetCDF is a binary,
+portable, self-describing file format on top of HDF5. The file format
+contents follow the AMBER NetCDF trajectory conventions
+(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions to this
+convention. This package implements a "dump nc"_dump_nc.html command
+and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
+in this format.  See src/USER-NC-DUMP/README for more details.
+
+NetCDF files can be directly visualized with the following tools:
+Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
+  and all of the above extensions. :ulb,l
+VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
+AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
+  a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+
+The person who created these files is Lars Pastewka at
+Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
+Contact him directly if you have questions.
+
+:line
+
 USER-OMP package :link(USER-OMP),h5

 Supporting info:
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@ -550,7 +550,8 @@ version = lmp.version()  # return the numerical version id, e.g. LAMMPS 2 Sep 20

 lmp.file(file)           # run an entire input script, file = "in.lj"
 lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100" :pre
-lmp.commands_list(cmdlist)  # invoke commands in cmdlist
+lmp.commands_list(cmdlist)     # invoke commands in cmdlist = ["run 10", "run 20"]
+lmp.commands_string(multicmd)  # invoke commands in multicmd = "run 10\nrun 20"

 xlo = lmp.extract_global(name,type)  # extract a global quantity
                                     # name = "boxxlo", "nlocal", etc
@ -631,8 +632,9 @@ lmp2 = lammps()
 lmp1.file("in.file1")
 lmp2.file("in.file2") :pre

-The file() and command() methods allow an input script or single
-commands to be invoked.
+The file(), command(), commands_list(), commands_string() methods
+allow an input script, a single command, or multiple commands to be
+invoked.

 The extract_global(), extract_atom(), extract_compute(),
 extract_fix(), and extract_variable() methods return values or
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -706,7 +706,7 @@ future changes to LAMMPS.
 User packages, such as user-atc or user-omp, have been contributed by
 users, and always begin with the user prefix.  If they are a single
 command (single file), they are typically in the user-misc package.
-Otherwise, they are a a set of files grouped together which add a
+Otherwise, they are a set of files grouped together which add a
 specific functionality to the code.

 User packages don't necessarily meet the requirements of the standard
@ -1601,9 +1601,9 @@ implementations, either by environment variables that specify how to
 order physical processors, or by config files that specify what
 physical processors to assign to each MPI rank.  The -reorder switch
 simply gives you a portable way to do this without relying on MPI
-itself.  See the "processors out"_processors command for how to output
-info on the final assignment of physical processors to the LAMMPS
-simulation domain.
+itself.  See the "processors out"_processors.html command for how
+to output info on the final assignment of physical processors to
+the LAMMPS simulation domain.

 -screen file :pre

--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -151,7 +151,7 @@ can start running so that the CPU pipeline is still being used
 efficiently. Although benefits can be seen by launching a MPI task
 for every hardware thread, for multinode simulations, we recommend
 that OpenMP threads are used for SMT instead, either with the
-USER-INTEL package, "USER-OMP package"_accelerate_omp.html", or
+USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or
 "KOKKOS package"_accelerate_kokkos.html. In the example above, up
 to 36X speedups can be observed by using all 36 physical cores with
 LAMMPS. By using all 72 hardware threads, an additional 10-30%
@ -343,7 +343,7 @@ when using offload.

 Not all styles are supported in the USER-INTEL package. You can mix
 the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
-package or the "USER-OMP package"_accelerate_omp.html". Of course,
+package or the "USER-OMP package"_accelerate_omp.html. Of course,
 this requires that these packages were installed at build time. This
 can performed automatically by using "-sf hybrid intel opt" or
 "-sf hybrid intel omp" command-line options. Alternatively, the "opt"
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@ -61,7 +61,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@ -65,11 +65,11 @@ more instructions on how to use the accelerated styles effectively.

 :line

-[Restrictions:] none
+[Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package.  See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.

 [Related commands:]

--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@ -76,7 +76,7 @@ for specific angle types.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other angle styles, the hybrid angle style does not store angle
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@ -147,7 +147,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@ -166,7 +166,7 @@ stores a per-particle mass and size and orientation (i.e. the corner
 points of the triangle).

 The {template} style allows molecular topolgy (bonds,angles,etc) to be
-defined via a molecule template using the "molecule"_molecule.txt
+defined via a molecule template using the "molecule"_molecule.html
 command.  The template stores one or more molecules with a single copy
 of the topology info (bonds,angles,etc) of each.  Individual atoms
 only store a template index and template atom to identify which
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@ -70,10 +70,10 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

-You typically should specify "special_bonds fene"_special_bonds.html"
+You typically should specify "special_bonds fene"_special_bonds.html
 or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
 style.  LAMMPS will issue a warning it that's not the case.

--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@ -73,10 +73,10 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

-You typically should specify "special_bonds fene"_special_bonds.html"
+You typically should specify "special_bonds fene"_special_bonds.html
 or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
 style.  LAMMPS will issue a warning it that's not the case.

--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@ -65,7 +65,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@ -59,7 +59,7 @@ bond types.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other bond styles, the hybrid bond style does not store bond
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@ -99,7 +99,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 The {quartic} style requires that "special_bonds"_special_bonds.html
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@ -144,7 +144,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/compute_centro_atom.txt
+++ b/doc/src/compute_centro_atom.txt
@ -114,7 +114,7 @@ local defects surrounding the central atom, as described above.  For
 the {axes yes} case, the vector components are also unitless, since
 they represent spatial directions.

-Here are typical centro-symmetry values, from a a nanoindentation
+Here are typical centro-symmetry values, from a nanoindentation
 simulation into gold (FCC).  These were provided by Jon Zimmerman
 (Sandia):

--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@ -536,7 +536,7 @@ For the {bin/cylinder} style the details are as follows.  If {discard}
 is set to {yes}, an out-of-domain atom will have its chunk ID set to
 0.  If {discard} is set to {no}, the atom will have its chunk ID set
 to the first or last bin in both the radial and axis dimensions.  If
-{discard} is set to {mixed}, which is the default, the the radial
+{discard} is set to {mixed}, which is the default, the radial
 dimension is treated the same as for {discard} = no.  But for the axis
 dimensinon, it will only have its chunk ID set to the first or last
 bin if bins extend to the simulation box boundary in the axis
--- a/doc/src/compute_fep.txt
+++ b/doc/src/compute_fep.txt
@ -236,7 +236,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 [Related commands:]

 "fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html,
-"pair_lj_soft_coul_soft"_pair_lj_soft_coul_soft.txt
+"pair_style lj/soft/coul/soft"_pair_lj_soft.html

 [Default:]

--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@ -15,7 +15,7 @@ compute ID group-ID orientorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 orientorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {cutoff} or {nnn} or {ql}
+keyword = {cutoff} or {nnn} or {degrees}
  {cutoff} value = distance cutoff
  {nnn} value = number of nearest neighbors
  {degrees} values = nlvalues, l1, l2,...  :pre
@ -111,7 +111,7 @@ options.

 [Default:]

-The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 9 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.

 :line

--- a/doc/src/compute_property_local.txt
+++ b/doc/src/compute_property_local.txt
@ -78,7 +78,7 @@ defined by the "pair_style"_pair_style.html command for the types of
 the two atoms is used.  For the {radius} setting, the sum of the radii
 of the two particles is used as a cutoff.  For example, this is
 appropriate for granular particles which only interact when they are
-overlapping, as computed by "granular pair styles"_pair_gran.txt.
+overlapping, as computed by "granular pair styles"_pair_gran.html.

 If the inputs are bond, angle, etc attributes, the local data is
 generated by looping over all the atoms owned on a processor and
--- a/doc/src/compute_stress_atom.txt
+++ b/doc/src/compute_stress_atom.txt
@ -60,7 +60,7 @@ produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
 atoms in a Tersoff 3-body interaction) is assigned in equal portions
 to each atom in the set.  E.g. 1/4 of the dihedral virial to each of
 the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
-to atoms in a a water molecule via the "fix shake"_fix_shake.html
+to atoms in a water molecule via the "fix shake"_fix_shake.html
 command.

 If no extra keywords are listed, all of the terms in this formula are
--- a/doc/src/compute_temp_profile.txt
+++ b/doc/src/compute_temp_profile.txt
@ -69,8 +69,8 @@ velocity for each atom.  Note that if there is only one atom in the
 bin, its thermal velocity will thus be 0.0.

 After the spatially-averaged velocity field has been subtracted from
-each atom, the temperature is calculated by the formula KE = (dim/2 N
- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of
+each atom, the temperature is calculated by the formula KE = (dim*N
+- dim*Nx*Ny*Nz) k T/2, where KE = total kinetic energy of the group of
 atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
 simulation, N = number of atoms in the group, k = Boltzmann constant,
 and T = temperature.  The dim*Nx*Ny*Nz term are degrees of freedom
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@ -109,7 +109,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@ -76,7 +76,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@ -69,7 +69,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_hybrid.txt
+++ b/doc/src/dihedral_hybrid.txt
@ -77,7 +77,7 @@ for specific dihedral types.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other dihedral styles, the hybrid dihedral style does not store
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@ -63,7 +63,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@ -71,7 +71,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_table.txt
+++ b/doc/src/dihedral_table.txt
@ -154,7 +154,7 @@ radians instead of degrees.  (Note: This changes the way the forces
 are scaled in the 4th column of the data file.)

 The optional "CHECKU" keyword is followed by a filename.  This allows
-the user to save all of the the {Ntable} different entries in the
+the user to save all of the {Ntable} different entries in the
 interpolated energy table to a file to make sure that the interpolated
 function agrees with the user's expectations.  (Note: You can
 temporarily increase the {Ntable} parameter to a high value for this
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@ -165,7 +165,7 @@ extra buffering.

 :line

-The {element} keyword applies only to the the dump {cfg}, {xyz}, and
+The {element} keyword applies only to the dump {cfg}, {xyz}, and
 {image} styles.  It associates element names (e.g. H, C, Fe) with
 LAMMPS atom types.  See the list of element names at the bottom of
 this page.
@ -574,7 +574,7 @@ e.g. its x-component of velocity if the atom-attribute "vx" was
 specified.

 The basic idea of a color map is that the atom-attribute will be
-within a range of values, and that range is associated with a a series
+within a range of values, and that range is associated with a series
 of colors (e.g. red, blue, green).  An atom's specific value (vx =
 -3.2) can then mapped to the series of colors (e.g. halfway between
 red and blue), and a specific color is determined via an interpolation
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@ -113,7 +113,7 @@ quantity being minimized), you MUST enable the
 [Restrictions:]

 This fix can only be used if LAMMPS was built with the MOLECULE
-package (which it is by default).  See the "Making
+package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@ -150,7 +150,7 @@ initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
 after 10 psec, the box length will have doubled.  After 20 psec, it
 will have tripled.

-The {erate} style changes a dimension of the the box at a "constant
+The {erate} style changes a dimension of the box at a "constant
 engineering strain rate".  The units of the specified strain rate are
 1/time.  See the "units"_units.html command for the time units
 associated with different choices of simulation units,
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@ -237,7 +237,7 @@ described in the papers cited below, the purpose of this method is to
 enable longer timesteps to be used (up to the numerical stability
 limit of the integrator), while still producing the correct Boltzmann
 distribution of atom positions.  It is implemented within LAMMPS, by
-changing how the the random force is applied so that it is composed of
+changing how the random force is applied so that it is composed of
 the average of two random forces representing half-contributions from
 the previous and current time intervals.

--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@ -233,7 +233,7 @@ present, the speed of sound squared is set equal to (1/3)*(dx/dt)^2.
 Setting a0 > (dx/dt)^2 is not allowed, as this may lead to
 instabilities.

-If the {noise} keyword is used, followed by a a positive temperature
+If the {noise} keyword is used, followed by a positive temperature
 value, and a positive integer random number seed, a thermal
 lattice-Boltzmann algorithm is used.  If {LBtype} is set equal to 1
 (i.e. the standard LB integrator is chosen), the thermal LB algorithm
--- a/doc/src/fix_phonon.txt
+++ b/doc/src/fix_phonon.txt
@ -184,7 +184,7 @@ This fix requires LAMMPS be built with an FFT library.  See the
 [Default:]

 The option defaults are sysdim = the same dimemsion as specified by
-the "dimension"_dimension command, and nasr = 20.
+the "dimension"_dimension.html command, and nasr = 20.

 :line

--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@ -177,7 +177,7 @@ their values.  This means that the values can be output via the "dump
 custom"_dump.html command, accessed by fixes like "fix
 ave/atom"_fix_ave_atom.html, accessed by other computes like "compute
 reduce"_compute_reduce.html, or used in "atom-style
-variables"_variables.
+variables"_variable.html.

 For example, these commands will output two new properties to a custom
 dump file:
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@ -8,6 +8,7 @@

 fix reax/bonds command :h3
 fix reax/c/bonds command :h3
+fix reax/c/bonds/kk command :h3

 [Syntax:]

@ -47,6 +48,31 @@ commands"_Section_howto.html#howto_15.  No parameter of this fix can
 be used with the {start/stop} keywords of the "run"_run.html command.
 This fix is not invoked during "energy minimization"_minimize.html.

+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section_accelerate"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section_accelerate"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]

 The fix reax/bonds command requires that the "pair_style
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@ -7,6 +7,7 @@
 :line

 fix reax/c/species command :h3
+fix reax/c/species/kk command :h3

 [Syntax:]

@ -129,6 +130,31 @@ No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.

+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section_accelerate"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section_accelerate"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]

 The fix species currently only works with
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@ -620,7 +620,7 @@ rigid styles for the rigid bodies. :l

 Use "fix press/berendsen"_fix_press_berendsen.html to compute the
 pressure and change the box dimensions.  Use one of the 4 NVE or 2 NVT
-rigid styles for the rigid bodies.  Use "fix nvt"_fix_nh.thml (or any
+rigid styles for the rigid bodies.  Use "fix nvt"_fix_nh.html (or any
 other thermostat) for the non-rigid particles. :l
 :ule

--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@ -87,7 +87,7 @@ end of each run. A positive value N means that the diagnostics are reported once
 per N time-steps.

 The diagnostics report the average # of integrator steps and RHS function evaluations
-and run-time per ODE as well as the the average/RMS/min/max per process. If the
+and run-time per ODE as well as the average/RMS/min/max per process. If the
 reporting frequency is 1, the RMS/min/max per ODE are also reported. The per ODE
 statistics can be used to adjust the tolerance and min/max step parameters. The
 statistics per MPI process can be useful to examine any load imbalance caused by the
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@ -28,7 +28,7 @@ fix 1 all smd/adjust_dt 0.1 :pre
 The fix calculates a new stable time increment for use with the SMD time integrators.

 The stable time increment is based on multiple conditions. For the SPH pair styles, a
-CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the the speed of
+CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the speed of
 sound cannot propagate further than a typical spacing between particles within a single time step to ensure
 no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a
 stable maximum time step.
--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@ -101,7 +101,7 @@ particles move in the normal way via a time integration "fix"_fix.html
 with a short timestep dt.  SRD particles advect with a large timestep
 dt_SRD >= dt.

-If the {lamda} keyword is not specified, the the SRD temperature
+If the {lamda} keyword is not specified, the SRD temperature
 {Tsrd} is used in the above formula to compute lamda.  If the {lamda}
 keyword is specified, then the {Tsrd} setting is ignored and the above
 equation is used to compute the SRD temperature.
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
@ -104,7 +104,7 @@ the Nose-Hoover thermostat ("fix nvt"_fix_nh.html) is {NOT}
 recommended due to its well documented issues with the canonical
 sampling of harmonic degrees of freedom (notice that the {chain}
 option will {NOT} solve this problem). The Langevin thermostat ("fix
-langevin"_fix_langevin.html") correctly thermostats the system and we
+langevin"_fix_langevin.html) correctly thermostats the system and we
 advise its usage with ti/spring command.

 [Restart, fix_modify, output, run start/stop, minimize info:]
--- a/doc/src/fix_ttm.txt
+++ b/doc/src/fix_ttm.txt
@ -107,7 +107,7 @@ specified as parameters to the fix.  The other quantities are derived.
 The form of the heat diffusion equation used here is almost the same
 as that in equation 6 of "(Duffy)"_#Duffy, with the exception that the
 electronic density is explicitly reprensented, rather than being part
-of the the specific heat parameter.
+of the specific heat parameter.

 Currently, fix ttm assumes that none of the user-supplied parameters
 will vary with temperature. Note that "(Duffy)"_#Duffy used a tanh()
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@ -77,7 +77,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@ -81,7 +81,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/improper_hybrid.txt
+++ b/doc/src/improper_hybrid.txt
@ -55,7 +55,7 @@ types.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other improper styles, the hybrid improper style does not store
--- a/doc/src/improper_style.txt
+++ b/doc/src/improper_style.txt
@ -27,7 +27,7 @@ between quadruplets of atoms, which remain in force for the duration
 of the simulation.  The list of improper quadruplets is read in by a
 "read_data"_read_data.html or "read_restart"_read_restart.html command
 from a data or restart file.  Note that the ordering of the 4 atoms in
-an improper quadruplet determines the the definition of the improper
+an improper quadruplet determines the definition of the improper
 angle used in the formula for each style.  See the doc pages of
 individual styles for details.

--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@ -83,9 +83,9 @@ replica.  Conceptually, the non-NEB atoms provide a background force
 field for the NEB atoms.  They can be allowed to move during the NEB
 minimiation procedure (which will typically induce different
 coordinates for non-NEB atoms in different replicas), or held fixed
-using other LAMMPS commands such as "fix setforce"_fix_setforce.  Note
-that the "partition"_partition.html command can be used to invoke a
-command on a subset of the replicas, e.g. if you wish to hold NEB or
+using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
+Note that the "partition"_partition.html command can be used to invoke
+a command on a subset of the replicas, e.g. if you wish to hold NEB or
 non-NEB atoms fixed in only the end-point replicas.

 The initial atomic configuration for each of the replicas can be
@ -284,7 +284,7 @@ ID2 x2 y2 z2
 ...
 IDN xN yN zN :pre

-The fields are the the atom ID, followed by the x,y,z coordinates.
+The fields are the atom ID, followed by the x,y,z coordinates.
 The lines can be listed in any order.  Additional trailing information
 on the line is OK, such as a comment.

--- a/doc/src/next.txt
+++ b/doc/src/next.txt
@ -44,7 +44,7 @@ one value from their respective list of values.  A {file}-style
 variable reads the next line from its associated file.  An
 {atomfile}-style variable reads the next set of lines (one per atom)
 from its associated file.  {String-} or {atom}- or {equal}- or
-{world}-style variables cannot be used with the the next command,
+{world}-style variables cannot be used with the next command,
 since they only store a single value.

 When any of the variables in the next command has no more values, a
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@ -168,7 +168,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).
+if LAMMPS was built with that package.

 [Related commands:]

--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@ -203,9 +203,8 @@ These pair styles can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair styles are part of the MANYBODY package.  They are only
-enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.

 These pair potentials require the "newton"_newton.html setting to be
 "on" for pair interactions.
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@ -382,7 +382,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair styles are part of the MANYBODY package.  They are only
-enabled if LAMMPS was built with that package (which it is by default).
+enabled if LAMMPS was built with that package.
 See the "Making LAMMPS"_Section_start.html#start_3 section for more
 info.

--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@ -174,9 +174,8 @@ respa"_run_style.html command.  They do not support the {inner},
 [Restrictions:]

 The {born/coul/long} style is part of the KSPACE package.  It is only
-enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.

 [Related commands:]

--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@ -186,9 +186,8 @@ respa"_run_style.html command.  They do not support the {inner},

 The {buck/coul/long} style is part of the KSPACE package.  The
 {buck/coul/long/cs} style is part of the CORESHELL package.  They are
-only enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+only enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.

 [Related commands:]

--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@ -156,7 +156,7 @@ These pair styles can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair styles are part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 These pair styles requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@ -313,9 +313,8 @@ This pair style can only be used via the {pair} keyword of the

 The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the
 KSPACE package.  The {coul/long/cs} style is part of the CORESHELL
-package.  They are only enabled if LAMMPS was built with that package
-(which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+package.  They are only enabled if LAMMPS was built with that package.
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 [Related commands:]

--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@ -412,9 +412,8 @@ The eam pair styles can only be used via the {pair} keyword of the
 [Restrictions:]

 All of these styles except the {eam/cd} style are part of the MANYBODY
-package.  They are only enabled if LAMMPS was built with that package
-(which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+package.  They are only enabled if LAMMPS was built with that package.
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 The {eam/cd} style is part of the USER-MISC package and also requires
 the MANYBODY package.  It is only enabled if LAMMPS was built with
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@ -159,7 +159,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This style is part of the MANYBODY package.  It is only enabled if
-LAMMPS was built with that package (which it is by default).
+LAMMPS was built with that package.

 [Related commands:]

--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@ -138,8 +138,8 @@ angle cutoff (degrees) :ul
 A single hydrogen atom type K can be specified, or a wild-card
 asterisk can be used in place of or in conjunction with the K
 arguments to select multiple types as hydrogens.  This takes the form
-"*" or "*n" or "n*" or "m*n".  See the "pair_coeff"_pair_coeff command
-doc page for details.
+"*" or "*n" or "n*" or "m*n".  See the "pair_coeff"_pair_coeff.html
+command doc page for details.

 If the donor flag is {i}, then the atom of type I in the pair_coeff
 command is treated as the donor, and J is the acceptor.  If the donor
--- a/doc/src/pair_lcbop.txt
+++ b/doc/src/pair_lcbop.txt
@ -72,7 +72,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair styles is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair potential requires the "newton"_newton.html setting to be
--- a/doc/src/pair_line_lj.txt
+++ b/doc/src/pair_line_lj.txt
@ -60,8 +60,8 @@ pair_style command or overridden with an optional argument in the
 pair_coeff command for a type pair as discussed below.  The distance
 between the centers of 2 line segments, or the center of a line
 segment and a point particle, must be less than this distance (plus
-the neighbor skin; see the "neighbor"_neighbor command), for the pair
-of particles to be included in the neighbor list.
+the neighbor skin; see the "neighbor"_neighbor.html command), for
+the pair of particles to be included in the neighbor list.

 NOTE: This means that a too-short value for the {cutoff} setting can
 exclude a pair of particles from the neighbor list even if pairs of
--- a/doc/src/pair_lubricateU.txt
+++ b/doc/src/pair_lubricateU.txt
@ -119,7 +119,7 @@ of walls (whether moving or stationary) will affect the volume
 fraction available to colloidal particles. This is currently accounted
 for with the following types of walls: "wall/lj93"_fix_wall.html,
 "wall/lj126"_fix_wall.html, "wall/colloid"_fix_wall.html, and
-"wall/harmonic_fix_wall.html".  For these wall styles, the correct
+"wall/harmonic"_fix_wall.html.  For these wall styles, the correct
 volume fraction will be used when walls do not coincide with the box
 boundary, as well as when walls move and thereby cause a change in the
 volume fraction. To use these wall styles with pair_style {lubricateU}
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@ -113,7 +113,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This pair style can only be used if LAMMPS was built with the MANYBODY
-package (which it is by default).  See the "Making
+package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/pair_polymorphic.txt
+++ b/doc/src/pair_polymorphic.txt
@ -191,7 +191,7 @@ input script. If using read_data, atomic masses must be defined in the
 atomic structure data file.

 This pair style is part of the MANYBODY package. It is only enabled if
-LAMMPS was built with that package (which it is by default). See the
+LAMMPS was built with that package. See the
 "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair potential requires the "newtion"_newton.html setting to be
--- a/doc/src/pair_srp.txt
+++ b/doc/src/pair_srp.txt
@ -99,7 +99,7 @@ The optional {exclude} keyword determines if forces are computed
 between first neighbor (directly connected) bonds.  For a setting of
 {no}, first neighbor forces are computed; for {yes} they are not
 computed. A setting of {no} cannot be used with the {min} option for
-distance calculation because the the minimum distance between directly
+distance calculation because the minimum distance between directly
 connected bonds is zero.

 Pair style {srp} turns off normalization of thermodynamic properties
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@ -192,7 +192,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@ -222,7 +222,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@ -156,7 +156,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@ -232,7 +232,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_thole.txt
+++ b/doc/src/pair_thole.txt
@ -180,7 +180,7 @@ package.
 langevin/drude"_fix_langevin_drude.html, "fix
 drude/transform"_fix_drude_transform.html, "compute
 temp/drude"_compute_temp_drude.html
-"pair_style lj/cut/coul/long"_pair_lj_cut_coul_long
+"pair_style lj/cut/coul/long"_pair_lj.html

 [Default:] none

--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@ -212,9 +212,8 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair style are part of the MANYBODY package.  They is only
-enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.

 These pair styles requires the "newton"_newton.html setting to be "on"
 for pair interactions.
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@ -214,7 +214,7 @@ when a correlated event occurs during the third stage of the loop
 listed above, i.e. when only one replica is running dynamics.

 When more than one replica detects an event at the end of the same
-event check (every {t_event} steps) during the the second stage, then
+event check (every {t_event} steps) during the second stage, then
 one of them is chosen at random.  The number of coincident events is
 the number of replicas that detected an event.  Normally, this value
 should be 1.  If it is often greater than 1, then either the number of
@ -241,7 +241,7 @@ time was spent in each stage (dephasing, dynamics, quenching, etc).

 Any "dump files"_dump.html defined in the input script, will be
 written to during a PRD run at timesteps corresponding to both
-uncorrelated and correlated events.  This means the the requested dump
+uncorrelated and correlated events.  This means the requested dump
 frequency in the "dump"_dump.html command is ignored.  There will be
 one dump file (per dump command) created for all partitions.

--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@ -188,7 +188,7 @@ is assumed to have been previously loaded by another python command.

 Note that the Python code that is loaded and run must contain a
 function with the specified {func} name.  To operate properly when
-later invoked, the the function code must match the {input} and
+later invoked, the function code must match the {input} and
 {return} and {format} keywords specified by the python command.
 Otherwise Python will generate an error.

--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@ -431,8 +431,8 @@ Atoms # sphere
 Pair Coeffs # lj/cut :pre

 will check if the currently-defined "atom_style"_atom_style.html is
-{sphere}, and the current "pair_style"_pair_style is {lj/cut}.  If
-not, LAMMPS will issue a warning to indicate that the data file
+{sphere}, and the current "pair_style"_pair_style.html is {lj/cut}.
+If not, LAMMPS will issue a warning to indicate that the data file
 section likely does not contain the correct number or type of
 parameters expected for the currently-defined style.

--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@ -185,7 +185,7 @@ For dump files in {xyz} format, only the {x}, {y}, and {z} fields are
 supported.  The dump file does not store atom IDs, so these are
 assigned consecutively to the atoms as they appear in the dump file,
 starting from 1.  Thus you should insure that order of atoms is
-consistent from snapshot to snapshot in the the XYZ dump file.  See
+consistent from snapshot to snapshot in the XYZ dump file.  See
 the "dump_modify sort"_dump_modify.html command if the XYZ dump file
 was written by LAMMPS.

@ -195,7 +195,7 @@ velocities, or their respective plugins may not support reading of
 velocities.  The molfile dump files do not store atom IDs, so these
 are assigned consecutively to the atoms as they appear in the dump
 file, starting from 1.  Thus you should insure that order of atoms are
-consistent from snapshot to snapshot in the the molfile dump file.
+consistent from snapshot to snapshot in the molfile dump file.
 See the "dump_modify sort"_dump_modify.html command if the dump file
 was written by LAMMPS.

@ -322,3 +322,6 @@ They are only enabled if LAMMPS was built with that packages.  See the

 The option defaults are box = yes, replace = yes, purge = no, trim =
 no, add = no, scaled = no, wrapped = yes, and format = native.
+
+:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
+
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@ -141,11 +141,11 @@ these settings after the restart file is read.
 "units"_units.html
 "newton bond"_newton.html (see discussion of newton command below)
 "atom style"_atom_style.html and "atom_modify"_atom_modify.html settings id, map, sort
-"comm style"_comm_style.html and "comm_modify"_comm_modify settings mode, cutoff, vel
+"comm style"_comm_style.html and "comm_modify"_comm_modify.html settings mode, cutoff, vel
 "timestep"_timestep.html
 simulation box size and shape and "boundary"_boundary.html settings
 atom "group"_group.html definitions
-per-type atom settings such as "mass"_mass.thml
+per-type atom settings such as "mass"_mass.html
 per-atom attributes including their group assignments and molecular topology attributes (bonds, angles, etc)
 force field styles ("pair"_pair_style.html, "bond"_bond_style.html, "angle"_angle_style.html, etc)
 force field coefficients ("pair"_pair_coeff.html, "bond"_bond_coeff.html, "angle"_angle_coeff.html, etc) in some cases (see below)
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@ -94,6 +94,13 @@ Of course this is also possible by not using any suffix commands, and
 explictly appending or not appending the suffix to the relevant
 commands in your input script.

+NOTE: The default "run_style"_run_style.html verlet is invoked prior to
+reading the input script and is therefore not affected by a suffix command
+in the input script. The KOKKOS package requires "run_style verlet/kk",
+so when using the KOKKOS package it is necessary to either use the command
+line "-sf kk" command or add an explicit "run_style verlet" command to the
+input script.
+
 [Restrictions:] none

 [Related commands:]
--- a/doc/src/tad.txt
+++ b/doc/src/tad.txt
@ -231,7 +231,7 @@ time was spent in each stage (NEB, dynamics, quenching, etc).

 Any "dump files"_dump.html defined in the input script will be written
 to during a TAD run at timesteps when an event is executed.  This
-means the the requested dump frequency in the "dump"_dump.html command
+means the requested dump frequency in the "dump"_dump.html command
 is ignored.  There will be one dump file (per dump command) created
 for all partitions.  The atom coordinates of the dump snapshot are
 those of the minimum energy configuration resulting from quenching
--- a/doc/src/thermo_style.txt
+++ b/doc/src/thermo_style.txt
@ -108,7 +108,7 @@ Style {custom} is the most general setting and allows you to specify
 which of the keywords listed above you want printed on each
 thermodynamic timestep.  Note that the keywords c_ID, f_ID, v_name are
 references to "computes"_compute.html, "fixes"_fix.html, and
-equal-style "variables"_variable.html" that have been defined
+equal-style "variables"_variable.html that have been defined
 elsewhere in the input script or can even be new styles which users
 have added to LAMMPS (see the "Section 10"_Section_modify.html
 section of the documentation).  Thus the {custom} style provides a
--- a/doc/src/tutorial_drude.txt
+++ b/doc/src/tutorial_drude.txt
@ -33,7 +33,7 @@ created by the surrounding particles.  Drude oscillators represent
 these dipoles by two fixed charges: the core (DC) and the Drude
 particle (DP) bound by a harmonic potential. The Drude particle can be
 thought of as the electron cloud whose center can be displaced from
-the position of the the corresponding nucleus.
+the position of the corresponding nucleus.

 The sum of the masses of a core-Drude pair should be the mass of the
 initial (unsplit) atom, \(m_C + m_D = m\).  The sum of their charges
--- a/doc/src/write_dump.txt
+++ b/doc/src/write_dump.txt
@ -26,7 +26,7 @@ write_dump all atom dump.atom
 write_dump subgroup atom dump.run.bin
 write_dump all custom dump.myforce.* id type x y vx fx
 write_dump flow custom dump.%.myforce id type c_myF\[3\] v_ke modify sort id
-write_dump all xyz system.xyz modify sort id elements O H
+write_dump all xyz system.xyz modify sort id element O H
 write_dump all image snap*.jpg type type size 960 960 modify backcolor white
 write_dump all image snap*.jpg element element &
   bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600  &
--- a/doc/utils/sphinx-config/conf.py
+++ b/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'
+

--- a/examples/COUPLE/simple/in.lj
+++ b/examples/COUPLE/simple/in.lj
@ -20,4 +20,6 @@ neigh_modify	delay 0 every 20 check no

 fix		1 all nve

+variable        fx atom fx
+
 run		10
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
sjplimp	77bbf03f0f	Merge pull request #252 from akohlmey/preinstalled-vs-scm remove the misleading "(which it is by default)" from several doc files	2016-11-04 10:59:06 -06:00
sjplimp	7cff08ca0a	Merge pull request #249 from lammps/unstable Incorporate merge commits from "unstable" into "master"	2016-11-04 10:58:55 -06:00
sjplimp	f0131393e0	Merge pull request #248 from akohlmey/collected-small-fixes collected small bugfixes and updates	2016-11-04 10:58:42 -06:00
sjplimp	32e0a58343	Merge pull request #247 from akohlmey/bounds-error-with-code-line Propagate error error locations for a few more utility functions	2016-11-04 10:58:14 -06:00
sjplimp	60908eeab4	Merge pull request #246 from akohlmey/manybody-short-neighbor-list Manybody short neighbor list	2016-11-04 10:57:43 -06:00
sjplimp	8214555b29	Merge pull request #244 from ketankhare/patch-2 Enable write_data for dihedral style fourier	2016-11-04 10:57:20 -06:00
Steve Plimpton	f48b71f46b	added examples/threebody, fix reaxc/speceies/kk	2016-11-04 10:56:04 -06:00
Axel Kohlmeyer	6cc4eb19af	remove the misleading "(which it is by default)" from several doc files	2016-11-04 12:20:17 -04:00
Axel Kohlmeyer	7d23a0737e	add thorough checking for valid arguments to -partition or -p	2016-11-04 00:42:23 -04:00
Axel Kohlmeyer	02510ec321	add temporary force accumulation to local variables for vashishta styles	2016-11-02 22:32:30 -04:00
Axel Kohlmeyer	33140e5004	accumulate forces in temporary local variables for tersoff	2016-11-02 22:16:53 -04:00
Axel Kohlmeyer	639fb6f444	use local variables for more efficient force accumulation	2016-11-02 17:20:56 -04:00
Axel Kohlmeyer	b156771721	build short neighbor list for sw on based on ij parameters only	2016-11-02 17:09:32 -04:00
Axel Kohlmeyer	5d787f7f16	avoid tiny memory leak, when the restart command is specified multiple times	2016-11-01 21:39:12 -04:00
Axel Kohlmeyer	c8f4b55588	avoid uninitialized data for using ewald/disp with lj only	2016-11-01 16:48:30 -04:00
Axel Kohlmeyer	e13e4031cf	avoid memory leak in pppm/disp/omp	2016-11-01 16:48:00 -04:00
Axel Kohlmeyer	782a328080	avoid memory leaks when using kspace solvers for lennard-jones	2016-11-01 14:55:13 -04:00
Axel Kohlmeyer	e81ae21dbd	do not access uninitialized data for ewald/disp and pppm/disp	2016-11-01 14:54:16 -04:00
Axel Kohlmeyer	7fdd6e2807	remove work repetitions for 'the'	2016-11-01 11:40:07 -04:00
Axel Kohlmeyer	2e0d304c7e	remove word repetitions for 'a'	2016-11-01 11:36:11 -04:00
Axel Kohlmeyer	c4b86a25a7	Merge branch 'master' into manybody-short-neighbor-list	2016-10-28 11:12:21 -04:00
Axel Kohlmeyer	218e121b41	Merge branch 'master' into bounds-error-with-code-line	2016-10-28 11:11:28 -04:00
Axel Kohlmeyer	93d393aa69	permission cleanup in tools folder	2016-10-28 10:48:35 -04:00
Axel Kohlmeyer	4216be49f3	Merge branch 'master' into collected-small-fixes	2016-10-28 10:46:33 -04:00
Axel Kohlmeyer	c3a1e72183	Version 27 Oct 2016	2016-10-27 11:40:36 -04:00
Steve Plimpton	d9891abdf4	new library functions	2016-10-27 09:34:04 -06:00
Axel Kohlmeyer	f9a9e27f5a	add error location propagation to atom->set_mass() and atom->check_mass()	2016-10-26 16:01:40 -04:00
Axel Kohlmeyer	35753b8f08	add error location propagation to force->bounds() and force->boundsbig()	2016-10-26 15:53:02 -04:00
Axel Kohlmeyer	f028a9a967	region cylinder is compatible with open_faces[2], so do not disallow it.	2016-10-26 15:04:18 -04:00
Axel Kohlmeyer	ef9f7c818e	fix off-by-one bug in buffer re-allocator	2016-10-26 10:14:08 -04:00
Axel Kohlmeyer	8e61bed2d8	add USER-OMP variant of manybody short neighbor list	2016-10-26 09:51:52 -04:00
Axel Kohlmeyer	3267b34590	simplify short neighbor list implementation. remove unneeded class member	2016-10-26 09:29:27 -04:00
Axel Kohlmeyer	0a417b4016	add short neighbor list support to pair style tersoff	2016-10-26 07:06:38 -04:00
Axel Kohlmeyer	399c0af150	consistent short neighbor list for vashishta and vashishta/table	2016-10-25 23:46:25 -04:00
Axel Kohlmeyer	e8b3f79690	fully tested multi-element compatible short neighbor list for Stillinger-Weber	2016-10-25 23:18:14 -04:00
ketankhare	7f3f5e8c38	Clean whitespace	2016-10-25 14:46:44 -04:00
ketankhare	f350500e69	Enable write_data	2016-10-25 14:43:12 -04:00
ketankhare	d7c77a419d	Enable write_data for dihedral_fourier	2016-10-25 14:36:18 -04:00
sjplimp	efaa8feab5	Merge pull request #239 from akohlmey/static-analysis-fixes Static analysis fixes	2016-10-25 10:32:55 -06:00
sjplimp	ad5f7c4581	Merge pull request #238 from giacomofiorin/colvars-2016-10-24 Colvars fixes and small changes	2016-10-25 10:32:41 -06:00
sjplimp	6b33499135	Merge pull request #231 from akohlmey/collected-doc-fixes Collected doc fixes	2016-10-25 10:30:34 -06:00
Axel Kohlmeyer	63eada2425	fix issue with docs for orientorder/atom compute reported by @andeplane this closes #243	2016-10-25 12:12:48 -04:00
Axel Kohlmeyer	1a436bd7a9	Merge branch 'collected-doc-fixes' of github.com:akohlmey/lammps into collected-doc-fixes	2016-10-25 11:58:42 -04:00
Axel Kohlmeyer	52dd9aee5f	Merge branch 'master' into collected-doc-fixes	2016-10-25 11:55:09 -04:00
Steve Plimpton	eca96e21ef	Merge branch 'doc'	2016-10-25 09:46:07 -06:00
Steve Plimpton	9c81ad1ab6	doc page changes	2016-10-25 09:45:55 -06:00
Axel Kohlmeyer	f8367e3d0f	update documentation pdf for updated colvars lib	2016-10-24 17:49:53 -04:00
Axel Kohlmeyer	ba6d1528bb	Merge branch 'colvars-2016-10-24' of https://github.com/giacomofiorin/lammps into colvars-update	2016-10-24 17:34:28 -04:00
Giacomo Fiorin	182141b850	Make SMP parallelism for Colvars optional	2016-10-24 17:13:34 -04:00
Axel Kohlmeyer	512c413b7e	whitespace cleanup	2016-10-24 17:13:21 -04:00
Axel Kohlmeyer	7b89e47a38	apply corrections to issues reported by static code analysis	2016-10-24 17:12:28 -04:00
Giacomo Fiorin	e02505c8cc	Add ensemble-biased metadynamics (Fabrizio Marinelli, NIH)	2016-10-24 17:11:09 -04:00
Giacomo Fiorin	be2d155cef	Minor changes and fixes not relevant to LAMMPS	2016-10-24 17:10:52 -04:00
Giacomo Fiorin	c243093980	Fix wall forces and subtractAppliedForce for extended-Lagrangian ABF	2016-10-24 17:05:47 -04:00
Giacomo Fiorin	ad57a17f48	Add C-linkage wrapper for colvarscript (useful with ctypes)	2016-10-24 16:48:20 -04:00
sjplimp	477ddaf112	Merge pull request #232 from akohlmey/small-bugfixes Small bugfixes	2016-10-24 08:15:08 -06:00
sjplimp	4f69d91a99	Merge pull request #230 from akohlmey/manual-in-ebook-format generate LAMMPS manual in ebook format	2016-10-24 08:12:08 -06:00
Axel Kohlmeyer	bc44988003	correct typo in write_dump docs this closes #233	2016-10-23 15:18:25 -04:00
Axel Kohlmeyer	db36c8bcc3	stop with error, if molecule command requires special bond auto-generation before box is defined	2016-10-21 14:51:09 -04:00
Axel Kohlmeyer	991034b632	have bond style table exit when bond length is outside table range	2016-10-21 14:01:06 -04:00
Axel Kohlmeyer	607246f923	ignore mobi file as well	2016-10-21 13:25:53 -04:00
Axel Kohlmeyer	6742fb634a	remove mobi file format creation from makefile and explain it in README instead	2016-10-21 12:05:21 -04:00
Axel Kohlmeyer	ed3f02f249	ignore generated PDF and ePUB files	2016-10-21 12:04:48 -04:00
Axel Kohlmeyer	a2e34aab0a	make certain, that atom->maxspecial is incremented with extra special space	2016-10-21 11:55:36 -04:00
Axel Kohlmeyer	6cd6c106ef	Merge branch 'collected-small-changes' into collected-doc-fixes	2016-10-20 19:27:18 -04:00
Axel Kohlmeyer	a9572275ee	Revert "support generation of manual in ePUB format" This reverts commit `8c3f5cb307`.	2016-10-20 16:27:00 -04:00
Axel Kohlmeyer	2cf77ff778	Add support for ebook generation in ePUB and mobi format	2016-10-20 16:16:17 -04:00
Axel Kohlmeyer	f022f6d88a	fix various formatting and broken link issues identified by ebook-convert	2016-10-20 14:40:18 -04:00
Axel Kohlmeyer	8c3f5cb307	support generation of manual in ePUB format	2016-10-20 09:27:26 -04:00
Axel Kohlmeyer	e8359923f1	update packages section in manual with information about USER-NC-DUMP	2016-10-19 15:58:50 -04:00
Axel Kohlmeyer	d2da0fabb4	Version 20 Oct 2016	2016-10-19 15:29:13 -04:00
Axel Kohlmeyer	13ce1037f2	Version 18 Oct 2016	2016-10-18 15:46:56 -04:00
Axel Kohlmeyer	fa984b2c3b	Version 13 Oct 2016	2016-10-13 19:56:33 -04:00
Axel Kohlmeyer	8540a9f038	Version 11 Oct 2016	2016-10-11 17:10:24 -04:00
Axel Kohlmeyer	13b6eb1bae	Version 6 Oct 2016	2016-10-06 19:12:58 -04:00
Axel Kohlmeyer	d80a9def17	Version 5 Oct 2016	2016-10-05 18:49:08 -04:00
Axel Kohlmeyer	be4734bdce	Version 30 Sep 2016	2016-09-30 11:57:15 -04:00
Axel Kohlmeyer	2551619b07	Version 29 Sep 2016	2016-09-29 10:55:26 -04:00
Axel Kohlmeyer	d8bf149edc	Version 28 Sep 2016	2016-09-29 10:55:18 -04:00
Axel Kohlmeyer	473b12ded4	Version 26 Sep 2016	2016-09-29 10:55:10 -04:00
Axel Kohlmeyer	27c3149590	Version 21 Sep 2016	2016-09-29 10:54:59 -04:00
Axel Kohlmeyer	3b408d71fe	Version 20 Sep 2016	2016-09-29 10:53:40 -04:00