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

remove the misleading "(which it is by default)" from several doc files

doc/.gitignore

@@ -1 +1,5 @@
 /html
+/LAMMPS.epub
+/LAMMPS.mobi
+/Manual.pdf
+/Developer.pdf

doc/Makefile

@@ -8,19 +8,21 @@ VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
 
 PYTHON        = $(shell which python3)
+HAS_PYTHON3    = NO
+HAS_VIRTUALENV = NO
 
-ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 1)
+ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
-$(error Python3 was not found! Please check README.md for further instructions)
+HAS_PYTHON3 = YES
 endif
 
-ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 1)
+ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
-$(error virtualenv was not found! Please check README.md for further instructions)
+HAS_VIRTUALENV = YES
 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
 
 # ------------------------------------------
 
@@ -30,6 +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"
@@ -61,6 +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; \
@@ -109,6 +126,8 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
 	)
 
 $(VENV):
+	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
+	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@( \
 		virtualenv -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \

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
 
@@ -92,5 +94,22 @@ 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/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="12 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
-12 Oct 2016 version :c,h4
+27 Oct 2016 version :c,h4
 
 Version info: :h4
 

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
@@ -528,6 +528,8 @@ These are additional commands in USER packages, which can be used if
 package"_Section_start.html#start_3.
 
 "dump custom/vtk"_dump_custom_vtk.html,
+"dump nc"_dump_nc.html,
+"dump nc/mpiio"_dump_nc.html,
 "group2ndx"_group2ndx.html,
 "ndx2group"_group2ndx.html :tb(c=3,ea=c)
 
@@ -573,6 +575,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "gcmc"_fix_gcmc.html,
 "gld"_fix_gld.html,
 "gravity (o)"_fix_gravity.html,
+"halt"_fix_halt.html,
 "heat"_fix_heat.html,
 "indent"_fix_indent.html,
 "langevin (k)"_fix_langevin.html,

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
+"neigh_modify"_neigh_modify.html command.  The safest settings are
-every 1 check yes".  Second, it may mean that an atom has moved far
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
-outside a processor's sub-domain or even the entire simulation box.
+moved far outside a processor's sub-domain or even the entire
-This indicates bad physics, e.g. due to highly overlapping atoms, too
+simulation box. This indicates bad physics, e.g. due to highly
-large a timestep, etc. :dd
+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
+"neigh_modify"_neigh_modify.html command.  The safest settings are
-every 1 check yes".  Second, it may mean that an atom has moved far
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
-outside a processor's sub-domain or even the entire simulation box.
+moved far outside a processor's sub-domain or even the entire
-This indicates bad physics, e.g. due to highly overlapping atoms, too
+simulation box. This indicates bad physics, e.g. due to highly
-large a timestep, etc. :dd
+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
+"neigh_modify"_neigh_modify.html command.  The safest settings are
-every 1 check yes".  Second, it may mean that an atom has moved far
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
-outside a processor's sub-domain or even the entire simulation box.
+moved far outside a processor's sub-domain or even the entire
-This indicates bad physics, e.g. due to highly overlapping atoms, too
+simulation box. This indicates bad physics, e.g. due to highly
-large a timestep, etc. :dd
+overlapping atoms, too large a timestep, etc. :dd
 
 {Overflow of allocated fix vector storage} :dt
 

doc/src/Section_howto.txt

@@ -1854,13 +1854,19 @@ internal LAMMPS operations.  Note that LAMMPS classes are defined
 within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
 application.
 
-Library.cpp contains these 5 basic functions:
+Library.cpp contains these functions for creating and destroying an
+instance of LAMMPS and sending it commands to execute.  See the
+documentation in the src/library.cpp file for details:
 
 void lammps_open(int, char **, MPI_Comm, void **)
+void lammps_open_no_mpi(int, char **, void **)
 void lammps_close(void *)
 int lammps_version(void *)
 void lammps_file(void *, char *)
-char *lammps_command(void *, char *) :pre
+char *lammps_command(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
 list of strings as if they were "command-line
@@ -1880,6 +1886,10 @@ half to the other code and run both codes simultaneously before
 syncing them up periodically.  Or it might instantiate multiple
 instances of LAMMPS to perform different calculations.
 
+The lammps_open_no_mpi() function is similar except that no MPI
+communicator is passed from the caller.  Instead, MPI_COMM_WORLD is
+used to instantiate LAMMPS, and MPI is initialzed if necessary.
+
 The lammps_close() function is used to shut down an instance of LAMMPS
 and free all its memory.
 
@@ -1891,44 +1901,93 @@ 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() and lammps_command() functions are used to pass a
+The lammps_file(), lammps_command(), lammps_commands_list(), and
-file or string to LAMMPS as if it were an input script or single
+lammps_commands_string() functions are used to pass one or more
-command in an input script.  Thus the calling code can read or
+commands to LAMMPS to execute, the same as if they were coming from an
-generate a series of LAMMPS commands one line at a time and pass it
+input script.
-thru the library interface to setup a problem and then run it,
-interleaving the lammps_command() calls with other calls to extract
-information from LAMMPS, perform its own operations, or call another
-code's library.
 
-Other useful functions are also included in library.cpp.  For example:
+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_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.
+
+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, 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 *) :pre
+
 int lammps_get_natoms(void *)
-void lammps_get_coords(void *, double *)
+void lammps_gather_atoms(void *, double *)
-void lammps_put_coords(void *, double *) :pre
+void lammps_scatter_atoms(void *, double *) :pre
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *) :pre
 
-These can extract various global or per-atom quantities from LAMMPS as
+The extract functions return a pointer to various global or per-atom
-well as values calculated by a compute, fix, or variable.  The
+quantities stored in LAMMPS or to values calculated by a compute, fix,
-"set_variable" function can set an existing string-style variable to a
+or variable.  The pointer returned by the extract_global() function
-new value, so that subsequent LAMMPS commands can access the variable.
+can be used as a permanent reference to a value which may change.  For
-The "get" and "put" operations can retrieve and reset atom
+the other extract functions, the underlying storage may be reallocated
-coordinates.  See the library.cpp file and its associated header file
+as LAMMPS runs, so you need to re-call the function to assure a
-library.h for details.
+current pointer or returned value(s).
 
-The key idea of the library interface is that you can write any
+The lammps_set_variable() function can set an existing string-style
-functions you wish to define how your code talks to LAMMPS and add
+variable to a new string value, so that subsequent LAMMPS commands can
-them to src/library.cpp and src/library.h, as well as to the "Python
+access the variable.  The lammps_get_thermo() function returns the
-interface"_Section_python.html.  The routines you add can access or
+current value of a thermo keyword as a double.
-change any LAMMPS data you wish.  The examples/COUPLE and python
+
-directories have example C++ and C and Python codes which show how a
+The lammps_get_natoms() function returns the total number of atoms in
-driver code can link to LAMMPS as a library, run LAMMPS on a subset of
+the system and can be used by the caller to allocate space for the
-processors, grab data from LAMMPS, change it, and put it back into
+lammps_gather_atoms() and lammps_scatter_atoms() functions.  The
-LAMMPS.
+gather function collects atom info of the requested type (atom coords,
+types, forces, etc) from all procsesors, orders them by atom ID, and
+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 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 added functions can access or
+change any LAMMPS data you wish.
 
 :line
 
@@ -2670,7 +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
@@ -2771,7 +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

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:

doc/src/Section_python.txt

@@ -534,10 +534,11 @@ from lammps import lammps :pre
 These are the methods defined by the lammps module.  If you look at
 the files src/library.cpp and src/library.h you will see that they
 correspond one-to-one with calls you can make to the LAMMPS library
-from a C++ or C or Fortran program.
+from a C++ or C or Fortran program, and which are described in
+"Section 6.19"_Section_howto.html#howto_19 of the manual.
 
 lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
-                         4 optional args are allowed: name, cmdargs, ptr, comm
+                         # 4 optional args are allowed: name, cmdargs, ptr, comm
 lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
 lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
 lmp = lammps(name="g++")   # create a LAMMPS object using the liblammps_g++.so library
@@ -549,6 +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 = ["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
@@ -580,6 +583,8 @@ var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
                                              #        1 = atom-style variable :pre
 
 flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
+value = lmp.get_thermo(name)              # return current value of a thermo keyword
+
 natoms = lmp.get_natoms()                 # total # of atoms as int
 data = lmp.gather_atoms(name,type,count)  # return atom attribute of all atoms gathered into data, ordered by atom ID
                                           # name = "x", "charge", "type", etc
@@ -599,9 +604,10 @@ create an instance of LAMMPS, wrapped in a Python class by the lammps
 Python module, and return an instance of the Python class as lmp.  It
 is used to make all subequent calls to the LAMMPS library.
 
-Additional arguments can be used to tell Python the name of the shared
+Additional arguments to lammps() can be used to tell Python the name
-library to load or to pass arguments to the LAMMPS instance, the same
+of the shared library to load or to pass arguments to the LAMMPS
-as if LAMMPS were launched from a command-line prompt.
+instance, the same as if LAMMPS were launched from a command-line
+prompt.
 
 If the ptr argument is set like this:
 
@@ -626,8 +632,9 @@ lmp2 = lammps()
 lmp1.file("in.file1")
 lmp2.file("in.file2") :pre
 
-The file() and command() methods allow an input script or single
+The file(), command(), commands_list(), commands_string() methods
-commands to be invoked.
+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

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
+itself.  See the "processors out"_processors.html command for how
-info on the final assignment of physical processors to the LAMMPS
+to output info on the final assignment of physical processors to
-simulation domain.
+the LAMMPS simulation domain.
 
 -screen file :pre
 

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"

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:]

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:]

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:]

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:]

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:]

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
+MOLECULE package.  See the "Making LAMMPS"_Section_start.html#start_3
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+section for more info on packages.
 
 [Related commands:]
 

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

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:]

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

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.
 

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.
 

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:]

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

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:]

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:]

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

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:]

doc/src/commands.txt

@@ -37,6 +37,7 @@ Commands :h1
    dump_image
    dump_modify
    dump_molfile
+   dump_nc
    echo
    fix
    fix_modify

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):
 

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

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:]
 

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
 

doc/src/compute_pe_atom.txt

@@ -72,9 +72,10 @@ compute        peratom all pe/atom
 compute        pe all reduce sum c_peratom
 thermo_style   custom step temp etotal press pe c_pe :pre
 
-NOTE: The per-atom energy does not any Lennard-Jones tail corrections
+NOTE: The per-atom energy does not include any Lennard-Jones tail
-invoked by the "pair_modify tail yes"_pair_modify.html command, since
+corrections to the energy added by the "pair_modify tail
-those are global contributions to the system energy.
+yes"_pair_modify.html command, since those are contributions to the
+global system energy.
 
 [Output info:]
 

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

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
@@ -133,6 +133,11 @@ compute        p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
 variable       press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
 thermo_style   custom step temp etotal press v_press :pre
 
+NOTE: The per-atom stress does not include any Lennard-Jones tail
+corrections to the pressure added by the "pair_modify tail
+yes"_pair_modify.html command, since those are contributions to the
+global system pressure.
+
 [Output info:]
 
 This compute calculates a per-atom array with 6 columns, which can be

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
+each atom, the temperature is calculated by the formula KE = (dim*N
-- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of
+- 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

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:]

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:]

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:]

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

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:]

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:]

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

doc/src/dump.txt

@@ -12,6 +12,7 @@ dump command :h3
 "dump image"_dump_image.html command :h3
 "dump movie"_dump_image.html command :h3
 "dump molfile"_dump_molfile.html command :h3
+"dump nc"_dump_nc.html command :h3
 
 [Syntax:]
 
@@ -43,7 +44,9 @@ args = list of arguments for a particular style :l
 
   {movie} args = discussed on "dump image"_dump_image.html doc page :pre
 
-  {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page :pre
+  {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page
+
+  {nc} args = discussed on "dump nc"_dump_nc.html doc page :pre
 
   {local} args = list of local attributes
     possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\]

doc/src/dump_modify.txt

@@ -47,9 +47,9 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
      id = sort per-atom lines by atom ID
      N = sort per-atom lines in ascending order by the Nth column
      -N = sort per-atom lines in descending order by the Nth column
-  {thresh} args = attribute operation value
+  {thresh} args = attribute operator value
     attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
-    operation = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
+    operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
     value = numeric value to compare to, or LAST
     these 3 args can be replaced by the word "none" to turn off thresholding
   {unwrap} arg = {yes} or {no} :pre
@@ -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.
@@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold.
 
 If an atom-style variable is used as the attribute, then it can
 produce continuous numeric values or effective Boolean 0/1 values
-which may be useful for the comparision operation.  Boolean values can
+which may be useful for the comparision operator.  Boolean values can
 be generated by variable formulas that use comparison or Boolean math
 operators or special functions like gmask() and rmask() and grmask().
 See the "variable"_variable.html command doc page for details.
@@ -503,11 +503,11 @@ less than 1/2 to greater than 1/2 (or vice versa) since the last dump.
 E.g. due to reactions and subsequent charge equilibration in a
 reactive force field.
 
-The choice of operations are the usual comparison operators.  The XOR
+The choice of operators listed above are the usual comparison
-operation (exclusive or) is also included as "|^".  In this context,
+operators.  The XOR operation (exclusive or) is also included as "|^".
-XOR means that if either the attribute or value is 0.0 and the other
+In this context, XOR means that if either the attribute or value is
-is non-zero, then the result is "true" and the threshold criterion is
+0.0 and the other is non-zero, then the result is "true" and the
-met.  Otherwise it is not met.
+threshold criterion is met.  Otherwise it is not met.
 
 :line
 
@@ -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

doc/src/dump_nc.txt

@@ -0,0 +1,66 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+dump nc command :h3
+dump nc/mpiio command :h3
+
+[Syntax:]
+
+dump ID group-ID nc N file.nc args
+dump ID group-ID nc/mpiio N file.nc args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be imaged :l
+{nc} or {nc/mpiio}  = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
+N = dump every this many timesteps :l
+file.nc = name of file to write to :l
+args = list of per atom data elements to dump, same as for the 'custom' dump style. :l,ule
+
+[Examples:]
+
+dump 1 all nc 100 traj.nc type x y z vx vy vz
+dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press :pre
+
+dump 1 all nc/mpiio 1000 traj.nc id type x y z :pre
+
+[Description:]
+
+Dump a snapshot of atom coordinates every N timesteps in Amber-style
+NetCDF file format. NetCDF files are binary, portable and
+self-describing.  This dump style will write only one file on the root
+node.  The dump style {nc} uses the "standard NetCDF
+library"_netcdf-home all data is collected on one processor and then
+written to the dump file. Dump style {nc/mpiio} used the "parallel
+NetCDF library"_pnetcdf-home and MPI-IO; it has better performance on
+a larger number of processors. Note that 'nc' outputs all atoms sorted
+by atom tag while 'nc/mpiio' outputs in order of the MPI rank.
+
+In addition to per-atom data, also global (i.e. not per atom, but per
+frame) quantities can be included in the dump file. This can be
+variables, output from computes or fixes data prefixed with v_, c_ and
+f_, respectively.  These properties are included via
+"dump_modify"_dump_modify.html {global}.
+
+:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
+:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
+
+:line
+
+[Restrictions:]
+
+The {nc} and {nc/mpiio} dump styles are part of the USER-NC-DUMP
+package.  It is only enabled if LAMMPS was built with that
+package. See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info.
+
+:line
+
+[Related commands:]
+
+"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
+

doc/src/fix.txt

@@ -190,6 +190,7 @@ of "this page"_Section_commands.html#cmd_5.
 "gcmc"_fix_gcmc.html - grand canonical insertions/deletions
 "gld"_fix_gcmc.html - generalized Langevin dynamics integrator
 "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
+"halt"_fix_halt.html - terminate a dynamics run or minimization
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
 "indent"_fix_indent.html - impose force due to an indenter
 "langevin"_fix_langevin.html - Langevin temperature control

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:]

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,

doc/src/fix_halt.txt

@@ -0,0 +1,121 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix halt command :h3
+
+[Syntax:]
+
+fix ID group-ID halt N attribute operator avalue keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+halt = style name of this fix command :l
+N = check halt condition every N steps :l
+attribute = hstyle or v_name :l
+  hstyle = {bondmax}
+  v_name = name of "equal-style variable"_variable.html :pre
+operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l
+avalue = numeric value to compare attribute to :l
+string = text string to print with optional variable names :l
+zero or more keyword/value pairs may be appended :l
+keyword = {error} :l
+  {error} value = {hard} or {soft} or {continue} :pre
+:ule
+
+[Examples:]
+
+fix 10 all halt 1 bondmax > 1.5
+fix 10 all print 10 v_myCheck != 0 error soft :pre
+
+[Description:]
+
+Check a condition every N steps during a simulation run.  N must be >=
+1.  If the condition is met, exit the run immediately.  In this
+context a "run" can be dynamics or minimization iterations, as
+specified by the "run"_run.html or "minimize"_minimize.html command.
+
+The specified group-ID is ignored by this fix.
+
+The specified {attribute} can be one of the {hstyle} options listed
+above, or an "equal-style variable"_variable.html referenced as
+{v_name}, where "name" is the name of a variable that has been defined
+previously in the input script.
+
+The only {hstyle} option currently implemented is {bondmax}.  This
+will loop over all bonds in the system, compute their current
+lengths, and set {attribute} to the longest bond distance.
+
+Equal-style variables evaluate to a numeric value.  See the
+"variable"_variable.html command for a description.  They calculate
+formulas which can involve mathematical operations, atom properties,
+group properties, thermodynamic properties, global values calculated
+by a "compute"_compute.html or "fix"_fix.html, or references to other
+"variables"_variable.html.  Thus they are a very general means of
+computing some attribute of the current system.  For example, the
+following "bondmax" variable will calculate the same quantity as the
+hstyle = bondmax option.
+
+compute         bdist all bond/local dist
+compute         bmax all reduce max c_bdist
+variable        bondmax equal c_bmax :pre
+
+Thus these two versions of a fix halt command will do the same thing:
+
+fix 10 all halt 1 bondmax > 1.5
+fix 10 all halt 1 v_bondmax > 1.5 :pre
+
+The version with "bondmax" will just run somewhat faster, due to less
+overhead in computing bond lengths and not storing them in a separate
+compute.
+
+The choice of operators listed above are the usual comparison
+operators.  The XOR operation (exclusive or) is also included as "|^".
+In this context, XOR means that if either the attribute or avalue is
+0.0 and the other is non-zero, then the result is "true".  Otherwise
+it is "false".
+
+The specified {avalue} must be a numeric value.
+
+:line
+
+The optional {error} keyword determines how the current run is halted.
+If its value is {hard}, then LAMMPS will stop with an error message.
+
+If its value is {soft}, LAMMPS will exit the current run, but continue
+to execute subsequent commands in the input script.  However,
+additional "run"_run.html or "minimize"_minimize.html commands will be
+skipped.  For example, this allows a script to output the current
+state of the system, e.g. via a "write_dump"_write_dump.html or
+"write_restart"_write_restart.html command.
+
+If its value is {continue}, the behavior is the same as for {soft},
+except subsequent subsequent "run"_run.html or
+"minimize"_minimize.html commands are executed.  This allows your
+script to remedy the condition that triggered the halt, if necessary.
+Note that you may wish use the "unfix"_unfix.html command on the fix
+halt ID, so that the same condition is not immediately triggered in a
+subsequent run.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output
+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.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"variable"_variable.html
+
+[Default:]
+
+The option defaults are error = hard.

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.
 

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

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
 

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:

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

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

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
 

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

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.

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.

doc/src/fix_temp_rescale.txt

@@ -54,7 +54,7 @@ name.  In this case, the variable will be evaluated each timestep, and
 its value used to determine the target temperature.
 
 Equal-style variables can specify formulas with various mathematical
-functions, and include "thermo_style"_thermox_style.html command
+functions, and include "thermo_style"_thermo_style.html command
 keywords for the simulation box parameters and timestep and elapsed
 time.  Thus it is easy to specify a time-dependent temperature.
 

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:]

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()

doc/src/fix_wall_gran_region.txt

@@ -163,16 +163,20 @@ info on how to re-specify a fix in an input script that reads a
 restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
 
-Note that info about region definitions is NOT included in restart
+NOTE: Information about region definitions is NOT included in restart
-files.  So you must re-define your region and if it is a moving
+files, as discussed on the "read_restart"_read_restart.html doc page.
-region, define its motion attributes in a way that is consistent with
+So you must re-define your region and if it is a moving region, define
-the simulation that wrote the restart file.  In particular, if you
+its motion attributes in a way that is consistent with the simulation
-want to change its motion attributes (e.g. its velocity), then you
+that wrote the restart file.  In particular, if you want to change the
-should insure the postition/orientation of the region at the initial
+region motion attributes (e.g. its velocity), then you should ensure
-restart timestep is the same as it was on the timestep the restart
+the postition/orientation of the region at the initial restart
-file was written.  If this is not possible, then you may need to
+timestep is the same as it was on the timestep the restart file was
-ignore info in the restart file by defining a new fix wall/gran/region
+written.  If this is not possible, you may need to ignore info in the
-command in your restart script (e.g. with a different fix ID).
+restart file by defining a new fix wall/gran/region command in your
+restart script, e.g. with a different fix ID.  Or if you want to keep
+the shear history info but discard the region motion information, you
+can use the same fix ID for fix wall/gran/region, but assign it a
+region with a different region ID.
 
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.  No global or per-atom quantities are stored by this fix for

doc/src/fixes.txt

@@ -48,6 +48,7 @@ Fixes :h1
    fix_gld
    fix_gle
    fix_gravity
+   fix_halt
    fix_heat
    fix_imd
    fix_indent

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:]

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:]

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

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.
 

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:]

doc/src/lammps.book

@@ -170,6 +170,7 @@ fix_gcmc.html
 fix_gld.html
 fix_gle.html
 fix_gravity.html
+fix_halt.html
 fix_heat.html
 fix_imd.html
 fix_indent.html

doc/src/minimize.txt

@@ -103,6 +103,11 @@ the line search fails because the step distance backtracks to 0.0
 the number of outer iterations or timesteps exceeds {maxiter}
 the number of total force evaluations exceeds {maxeval} :ul
 
+NOTE: You can also use the "fix halt"_fix_halt.html command to specify
+a general criterion for exiting a minimization, that is a calculation
+performed on the state of the current system, as defined by an
+"equal-style variable"_variable.html.
+
 For the first criterion, the specified energy tolerance {etol} is
 unitless; it is met when the energy change between successive
 iterations divided by the energy magnitude is less than or equal to

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
+using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
-that the "partition"_partition.html command can be used to invoke a
+Note that the "partition"_partition.html command can be used to invoke
-command on a subset of the replicas, e.g. if you wish to hold NEB or
+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.
 

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

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:]
 

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
+enabled if LAMMPS was built with that package.  See the
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
-for more info.
 
 These pair potentials require the "newton"_newton.html setting to be
 "on" for pair interactions.

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.
 

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
+enabled if LAMMPS was built with that package.  See the
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
-for more info.
 
 [Related commands:]
 

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
+only enabled if LAMMPS was built with that package.  See the
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
-for more info.
 
 [Related commands:]
 

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"

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
+package.  They are only enabled if LAMMPS was built with that package.
-(which it is by default).  See the "Making
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
-LAMMPS"_Section_start.html#start_3 section for more info.
 
 [Related commands:]
 

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

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:]
 

doc/src/pair_gauss.txt

@@ -106,8 +106,31 @@ more instructions on how to use the accelerated styles effectively.
 
 [Mixing, shift, table, tail correction, restart, rRESPA info]:
 
-These pair styles do not support mixing. Thus, coefficients for all
+For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh
-I,J pairs must be specified explicitly.
+parameters, and the cutoff distance for these pair styles can be mixed:
+A (energy units)
+sqrt(1/B) (distance units, see below)
+H (energy units)
+sigma_h (distance units)
+r_mh (distance units)
+cutoff (distance units):ul
+
+The default mix value is {geometric}.
+Only {arithmetic} and {geometric} mix values are supported.
+See the "pair_modify" command for details.
+
+The A and H parameters are mixed using the same rules normally
+used to mix the "epsilon" parameter in a Lennard Jones interaction.
+The sigma_h, r_mh, and the cutoff distance are mixed using the same
+rules used to mix the "sigma" parameter in a Lennard Jones interaction.
+The B parameter is converted to a distance (sigma), before mixing
+(using sigma=B^-0.5), and converted back to a coefficient
+afterwards (using B=sigma^2).
+Negative A values are converted to positive A values (using abs(A))
+before mixing, and converted back after mixing
+(by multiplying by sign(Ai)*sign(Aj)).
+This way, if either particle is repulsive (if Ai<0 or Aj<0),
+then the default interaction between both particles will be repulsive.
 
 The {gauss} style does not support the "pair_modify"_pair_modify.html
 shift option. There is no effect due to the Gaussian well beyond the

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
+"*" or "*n" or "n*" or "m*n".  See the "pair_coeff"_pair_coeff.html
-doc page for details.
+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

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

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
+the neighbor skin; see the "neighbor"_neighbor.html command), for
-of particles to be included in the neighbor list.
+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

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}

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:]

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

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

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"

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"

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"

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"

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
 

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
+enabled if LAMMPS was built with that package.  See the
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
-for more info.
 
 These pair styles requires the "newton"_newton.html setting to be "on"
 for pair interactions.