patch 4May17

Fixing auto_sync logic bug in modify_kokkos

bench/FERMI/README

@@ -14,7 +14,7 @@ lmp_linux_mixed
 lmp_linux_double
 
 The precision (single, mixed, double) refers to the GPU and USER-CUDA
-pacakge precision.  See the README files in the lib/gpu and lib/cuda
+package precision.  See the README files in the lib/gpu and lib/cuda
 directories for instructions on how to build the packages with
 different precisions.  The GPU and USER-CUDA sub-sections of the
 doc/Section_accelerate.html file also describes this process.

doc/.gitignore

@@ -1,4 +1,5 @@
 /html
+/spelling
 /LAMMPS.epub
 /LAMMPS.mobi
 /Manual.pdf

doc/Makefile

@@ -6,6 +6,7 @@ BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
 VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
+ANCHORCHECK   = $(VENV)/bin/doc_anchor_check
 
 PYTHON        = $(shell which python3)
 HAS_PYTHON3    = NO
@@ -22,7 +23,7 @@ endif
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub html pdf old venv
+.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
 
 # ------------------------------------------
 
@@ -36,6 +37,7 @@ help:
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
+	@echo "  anchor_check  scan for duplicate anchor labels"
 
 # ------------------------------------------
 
@@ -44,12 +46,19 @@ clean-all:
 
 clean:
 	rm -rf $(RSTDIR) html
+	rm -rf spelling
 
-html: $(OBJECTS)
+clean-spelling:
+	rm -rf spelling
+
+html: $(OBJECTS) $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		echo "############################################" ;\
+		doc_anchor_check src/*.txt ;\
+		echo "############################################" ;\
 		deactivate ;\
 	)
 	-rm html/searchindex.js
@@ -64,6 +73,17 @@ html: $(OBJECTS)
 	@rm -rf html/USER/*/*.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
+spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
+	@(\
+		. $(VENV)/bin/activate ;\
+		pip install sphinxcontrib-spelling ;\
+		cp -r src/* $(RSTDIR)/ ;\
+        cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
+		sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
+		deactivate ;\
+	)
+	@echo "Spell check finished."
+
 epub: $(OBJECTS)
 	@mkdir -p epub
 	@rm -f LAMMPS.epub
@@ -112,6 +132,13 @@ fetch:
 
 txt2html: utils/txt2html/txt2html.exe
 
+anchor_check : $(ANCHORCHECK)
+	@(\
+		. $(VENV)/bin/activate ;\
+		doc_anchor_check src/*.txt ;\
+		deactivate ;\
+	)
+
 # ------------------------------------------
 
 utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
@@ -136,7 +163,7 @@ $(VENV):
 		deactivate;\
 	)
 
-$(TXT2RST): $(VENV)
+$(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \
 		(cd utils/converters;\

doc/src/2001/input_commands.html

@@ -464,7 +464,7 @@ the angletype option can only be assigned to a "fix style" of "shake",
   entirely rigid (e.g. water)
 the angletype option enables an additional check when SHAKE constraints
   are computed: if a cluster is of size 3 and both bonds in
-  the cluster are of a bondtype specified by the 2nd paramter of
+  the cluster are of a bondtype specified by the 2nd parameter of
   angletype, then the cluster is SHAKEn with an additional angle
   constraint that makes it rigid, using the equilibrium angle appropriate
   to the specified angletype
@@ -476,7 +476,7 @@ IMPORTANT NOTE: the angletype option has one additional affect, namely
   since they will not be SHAKEn but neither will the angle force by computed
 for style region, a coeff of INF means + or - infinity (all the way 
   to the boundary)
-an atom can be assigned to multiple constraints, the contraints will be
+an atom can be assigned to multiple constraints, the constraints will be
   applied in the reverse order they are assigned to that atom
   (e.g. each timestep, the last fix assigned to an atom will be applied 
   to it first, then the next-to-last applied second, etc)
@@ -689,7 +689,7 @@ coeffs:  types
          remainder
                no other parameters required
        
-used with "create temp" commmand to initialize velocities of atoms
+used with "create temp" command to initialize velocities of atoms
 by default, the "create temp" command initializes the velocities of all atoms,
   this command limits the initialization to a group of atoms
 this command is only in force for the next "create temp" command, any
@@ -1263,7 +1263,7 @@ when using constraints with the minimizer, fixes are
   applied when atoms move except for the following
 fixes associated with temperature control are not allowed
   (rescale, hoover/drag, langevin)
-the minimizer does not invoke the "fix style shake" contraints on
+the minimizer does not invoke the "fix style shake" constraints on
   bond lengths
 the minimizer does not invoke pressure control or volume control settings
 for good convergence, should specify use of smooth nonbond force fields 
@@ -1566,7 +1566,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any sizes
   can be used that are supported by native machine libraries
 this command is optional - if not used, a default
   mesh size will be chosen to satisfy accuracy criterion - if used, the
-  specifed mesh size will override the default
+  specified mesh size will override the default
 </PRE>
 <HR>
 <H3>
@@ -1788,7 +1788,7 @@ if the style is 2, restart information will be written alternately to files
 when the minimizer is invoked this command means create a restart file
   at the end of the minimization with the filename filename.timestep.min
 a restart file stores atom and force-field information in binary form
-allows program to restart from where it left off (see &quot;read restart&quot; commmand)
+allows program to restart from where it left off (see &quot;read restart&quot; command)
 
 Default = 0
 </PRE>

doc/src/99/basics.html

@@ -167,7 +167,7 @@ tool on the small-system data file.</P>
 <P>
 (6) flow</P>
 <P>
-2-d flow of Lennard-Jones atoms in a channel using various contraint 
+2-d flow of Lennard-Jones atoms in a channel using various constraint
 options.</P>
 <P>
 (7) polymer</P>
@@ -201,7 +201,7 @@ The tools directory also has a F77 program called setup_chain.f
 (compile and link with print.c) which can be used to generate random 
 initial polymer configurations for bead-spring models like those used 
 in examples/polymer. It uses an input polymer definition file (see 
-examples/polymer for two sample def files) that specfies how many 
+examples/polymer for two sample def files) that specifies how many
 chains of what length, a random number seed, etc.</P>
 </BODY>
 </HTML>

doc/src/99/crib.html

@@ -40,7 +40,7 @@ Note: this file is somewhat out-of-date for LAMMPS 99.</P>
     <LI>
     maxtype = max # of atom types 
     <LI>
-    maxbond = max # of bonds to compute on one procesor 
+    maxbond = max # of bonds to compute on one processor
     <LI>
     maxangle = max # of angles to compute on one processor 
     <LI>

doc/src/99/input_commands.html

@@ -294,7 +294,7 @@ assign a group of atoms to a particular constraint
 use appropriate number of coeffs for a particular style
 the constraint itself is defined by the "fix style" command
 multiple groups of atoms can be assigned to the same constraint
-an atom can be assigned to multiple constraints, the contraints will be
+an atom can be assigned to multiple constraints, the constraints will be
   applied in the reverse order they are assigned to that atom
   (e.g. each timestep, the last fix assigned to an atom will be applied 
   to it first, then the next-to-last applied second, etc)
@@ -477,7 +477,7 @@ coeffs:  types
          remainder
                no other parameters required
        
-used with "create temp" commmand to initialize velocities of atoms
+used with "create temp" command to initialize velocities of atoms
 by default, the "create temp" command initializes the velocities of all atoms,
   this command limits the initialization to a group of atoms
 this command is only in force for the next "create temp" command, any
@@ -1124,7 +1124,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any size
   can be used that are supported by native machine libraries
 this command is optional - if not used, a default
   mesh size will be chosen to satisfy accuracy criterion - if used, the
-  specifed mesh size will override the default
+  specified mesh size will override the default
 
 Default = none
 </PRE>
@@ -1343,7 +1343,7 @@ value of 0 means never create one
 program will toggle between 2 filenames as the run progresses
   so always have at least one good file even if the program dies in mid-write
 restart file stores atom positions and velocities in binary form
-allows program to restart from where it left off (see &quot;read restart&quot; commmand)
+allows program to restart from where it left off (see &quot;read restart&quot; command)
 
 Default = 0
 </PRE>

doc/src/Eqs/fix_gcmc1.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\mu &=&\mu^{id} + \mu^{ex}
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/fix_gcmc2.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\mu^{id} &=& k T \ln{\rho \Lambda^3} \\
+&=& k T \ln{\frac{\phi P \Lambda^3}{k T}} 
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/fix_gcmc3.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\Lambda &=& \sqrt{ \frac{h^2}{2 \pi m k T}}
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_kolmogorov_crespi_z.tex

@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+\thispagestyle{empty}
+
+\begin{document}
+
+\begin{eqnarray*}
+  E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
+  V_{ij} & = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\
+  \rho_{ij}^2 = \rho_{ji}^2 & = &  x_{ij}^2 + y_{ij}^2 ~\hspace{2cm} (\mathbf{n_i}\equiv\hat \mathbf{z})\\
+  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right) ^{2n}
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_momb.tex

@@ -0,0 +1,13 @@
+\documentclass[12pt,fleqn]{article}
+\usepackage{amsmath}
+\thispagestyle{empty}
+
+\begin{document}
+
+\setlength{\jot}{2ex}
+\begin{gather*}
+  E = D_0 [\exp^{-2 \alpha (r-r_0)} - 2\exp^{-\alpha (r-r_0)}] - s_6 \frac{C_6}{r^6} f_{damp}(r,R_r) \\
+  f_{damp}(r,R_r) = \frac{1}{1 + \exp^{-d(r/R_r - 1)}}
+\end{gather*}
+
+\end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="26 Jan 2017 version">
+<META NAME="docnumber" CONTENT="4 May 2017 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
-26 Jan 2017 version :c,h4
+4 May 2017 version :c,h4
 
 Version info: :h4
 
@@ -39,7 +39,7 @@ directory name created when you unpack a tarball, and at the top of
 the first page of the manual (this page).
 
 If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current version of LAMMPS. :ulb,l
+describe the most current [development] version of LAMMPS. :ulb,l
 
 If you browse the HTML doc pages included in your tarball, they
 describe the version you have. :l
@@ -67,7 +67,7 @@ Labs and Temple University:
 
 "Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l
 Aidan Thompson, athomps at sandia.gov :l
-Stan Moore, stamoore at sandia.gov :l
+Stan Moore, stamoor at sandia.gov :l
 "Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
 :ule
 
@@ -158,12 +158,11 @@ END_RST -->
   2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
   2.2 "Making LAMMPS"_start_2 :b
   2.3 "Making LAMMPS with optional packages"_start_3 :b
-  2.4 "Building LAMMPS via the Make.py script"_start_4 :b
-  2.5 "Building LAMMPS as a library"_start_5 :b
-  2.6 "Running LAMMPS"_start_6 :b
-  2.7 "Command-line options"_start_7 :b
-  2.8 "Screen output"_start_8 :b
-  2.9 "Tips for users of previous versions"_start_9 :ule,b
+  2.4 "Building LAMMPS as a library"_start_4 :b
+  2.5 "Running LAMMPS"_start_5 :b
+  2.6 "Command-line options"_start_6 :b
+  2.7 "Screen output"_start_7 :b
+  2.8 "Tips for users of previous versions"_start_8 :ule,b
 "Commands"_Section_commands.html :l
   3.1 "LAMMPS input script"_cmd_1 :ulb,b
   3.2 "Parsing rules"_cmd_2 :b

doc/src/Section_commands.txt

@@ -281,12 +281,12 @@ the "minimize"_minimize.html command.  A parallel tempering
 
 3.4 Commands listed by category :link(cmd_4),h4
 
-This section lists all LAMMPS commands, grouped by category.  The
-"next section"_#cmd_5 lists the same commands alphabetically.  The
+This section lists core LAMMPS commands, grouped by category.
+The "next section"_#cmd_5 lists all commands alphabetically.  The
 next section also includes (long) lists of style options for entries
 that appear in the following categories as a single command (fix,
 compute, pair, etc).  Commands that are added by user packages are not
-included in these categories, but they are in the next section.
+included in the categories here, but they are in the next section.
 
 Initialization:
 
@@ -361,7 +361,7 @@ Settings:
 "timer"_timer.html,
 "timestep"_timestep.html
 
-Operations within timestepping (fixes) and diagnositics (computes):
+Operations within timestepping (fixes) and diagnostics (computes):
 
 "compute"_compute.html,
 "compute_modify"_compute_modify.html,
@@ -687,6 +687,7 @@ package"_Section_start.html#start_3.
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
 "eos/table/rx"_fix_eos_table_rx.html,
+"filter/corotate"_fix_filter_corotate.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
 "grem"_fix_grem.html,
@@ -939,6 +940,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
 "lj/charmm/coul/long (giko)"_pair_charmm.html,
 "lj/charmm/coul/msm"_pair_charmm.html,
+"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
+"lj/charmmfsw/coul/long"_pair_charmm.html,
 "lj/class2 (gko)"_pair_class2.html,
 "lj/class2/coul/cut (ko)"_pair_class2.html,
 "lj/class2/coul/long (gko)"_pair_class2.html,
@@ -969,7 +972,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lubricateU/poly"_pair_lubricateU.html,
 "meam"_pair_meam.html,
 "mie/cut (o)"_pair_mie.html,
-"morse (got)"_pair_morse.html,
+"morse (gkot)"_pair_morse.html,
 "nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
 "nm/cut (o)"_pair_nm.html,
 "nm/cut/coul/cut (o)"_pair_nm.html,
@@ -1016,6 +1019,7 @@ package"_Section_start.html#start_3.
 "eff/cut"_pair_eff.html,
 "exp6/rx"_pair_exp6_rx.html,
 "gauss/cut"_pair_gauss.html,
+"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "lennard/mdf"_pair_mdf.html,
 "list"_pair_list.html,
 "lj/charmm/coul/long/soft (o)"_pair_charmm.html,
@@ -1033,6 +1037,7 @@ package"_Section_start.html#start_3.
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.html,
+"momb"_pair_momb.html,
 "morse/smooth/linear"_pair_morse.html,
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
@@ -1042,8 +1047,12 @@ package"_Section_start.html#start_3.
 "oxdna/hbond"_pair_oxdna.html,
 "oxdna/stk"_pair_oxdna.html,
 "oxdna/xstk"_pair_oxdna.html,
+"oxdna2/coaxstk"_pair_oxdna2.html,
+"oxdna2/dh"_pair_oxdna2.html,
+"oxdna2/excv"_pair_oxdna2.html,
+"oxdna2/stk"_pair_oxdna2.html,
 "quip"_pair_quip.html,
-"reax/c (k)"_pair_reax_c.html,
+"reax/c (k)"_pair_reaxc.html,
 "smd/hertz"_pair_smd_hertz.html,
 "smd/tlsph"_pair_smd_tlsph.html,
 "smd/triangulated/surface"_pair_smd_triangulated_surface.html,
@@ -1059,7 +1068,7 @@ package"_Section_start.html#start_3.
 "table/rx"_pair_table_rx.html,
 "tersoff/table (o)"_pair_tersoff.html,
 "thole"_pair_thole.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
+"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) 
 
 :line
 
@@ -1076,7 +1085,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "none"_bond_none.html,
 "zero"_bond_zero.html,
 "hybrid"_bond_hybrid.html,
-"class2 (o)"_bond_class2.html,
+"class2 (ko)"_bond_class2.html,
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
 "harmonic (ko)"_bond_harmonic.html,
@@ -1091,7 +1100,8 @@ package"_Section_start.html#start_3.
 
 "harmonic/shift (o)"_bond_harmonic_shift.html,
 "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
+"oxdna/fene"_bond_oxdna.html,
+"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c)
 
 :line
 
@@ -1109,7 +1119,7 @@ USER-OMP, t = OPT.
 "zero"_angle_zero.html,
 "hybrid"_angle_hybrid.html,
 "charmm (ko)"_angle_charmm.html,
-"class2 (o)"_angle_class2.html,
+"class2 (ko)"_angle_class2.html,
 "cosine (o)"_angle_cosine.html,
 "cosine/delta (o)"_angle_cosine_delta.html,
 "cosine/periodic (o)"_angle_cosine_periodic.html,
@@ -1145,7 +1155,8 @@ USER-OMP, t = OPT.
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
 "charmm (ko)"_dihedral_charmm.html,
-"class2 (o)"_dihedral_class2.html,
+"charmmfsw"_dihedral_charmm.html,
+"class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
 "helix (o)"_dihedral_helix.html,
 "multi/harmonic (o)"_dihedral_multi_harmonic.html,
@@ -1177,7 +1188,7 @@ USER-OMP, t = OPT.
 "none"_improper_none.html,
 "zero"_improper_zero.html,
 "hybrid"_improper_hybrid.html,
-"class2 (o)"_improper_class2.html,
+"class2 (ko)"_improper_class2.html,
 "cvff (io)"_improper_cvff.html,
 "harmonic (ko)"_improper_harmonic.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

doc/src/Section_errors.txt

@@ -22,7 +22,7 @@ either conceptually, or as printed out by the program.
 
 12.1 Common problems :link(err_1),h4
 
-If two LAMMPS runs do not produce the same answer on different
+If two LAMMPS runs do not produce the exact same answer on different
 machines or different numbers of processors, this is typically not a
 bug.  In theory you should get identical answers on any number of
 processors and on any machine.  In practice, numerical round-off can
@@ -80,12 +80,24 @@ order.  If you mess this up, LAMMPS will often flag the error, but it
 may also simply read a bogus argument and assign a value that is
 valid, but not what you wanted.  E.g. trying to read the string "abc"
 as an integer value of 0.  Careful reading of the associated doc page
-for the command should allow you to fix these problems.  Note that
-some commands allow for variables to be specified in place of numeric
-constants so that the value can be evaluated and change over the
-course of a run.  This is typically done with the syntax {v_name} for
-a parameter, where name is the name of the variable.  This is only
-allowed if the command documentation says it is.
+for the command should allow you to fix these problems. In most cases,
+where LAMMPS expects to read a number, either integer or floating point,
+it performs a stringent test on whether the provided input actually
+is an integer or floating-point number, respectively, and reject the
+input with an error message (for instance, when an integer is required,
+but a floating-point number 1.0 is provided):
+
+ERROR: Expected integer parameter in input script or data file :pre
+
+Some commands allow for using variable references in place of numeric
+constants so that the value can be evaluated and may change over the
+course of a run.  This is typically done with the syntax {v_name} for a
+parameter, where name is the name of the variable. On the other hand,
+immediate variable expansion with the syntax ${name} is performed while
+reading the input and before parsing commands,
+
+NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
+the documentation of the corresponding command explicitly says it is.
 
 Generally, LAMMPS will print a message to the screen and logfile and
 exit gracefully when it encounters a fatal error.  Sometimes it will
@@ -562,11 +574,11 @@ group of atoms correctly. :dd
 
 {Bad quadratic solve for particle/line collision} :dt
 
-This is an internal error.  It should nornally not occur. :dd
+This is an internal error.  It should normally not occur. :dd
 
 {Bad quadratic solve for particle/tri collision} :dt
 
-This is an internal error.  It should nornally not occur. :dd
+This is an internal error.  It should normally not occur. :dd
 
 {Bad real space Coulomb cutoff in fix tune/kspace} :dt
 
@@ -900,7 +912,7 @@ Atoms can not be added afterwards to this fix option. :dd
 
 {Cannot append atoms to a triclinic box} :dt
 
-The simulation box must be defined with edges alligned with the
+The simulation box must be defined with edges aligned with the
 Cartesian axes. :dd
 
 {Cannot balance in z dimension for 2d simulation} :dt
@@ -980,7 +992,7 @@ file. :dd
 
 LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6
 factor that partitions the computation between real space and k-space
-for Disptersion interactions. :dd
+for Dispersion interactions. :dd
 
 {Cannot create an atom map unless atoms have IDs} :dt
 
@@ -1315,7 +1327,7 @@ Self-explanatory. :dd
 
 This file is created when you use some LAMMPS features, to indicate
 what paper you should cite on behalf of those who implemented
-the feature.  Check that you have write priveleges into the directory
+the feature.  Check that you have write privileges into the directory
 you are running in. :dd
 
 {Cannot open log.lammps for writing} :dt
@@ -1993,7 +2005,7 @@ Self-explanatory. :dd
 
 {Cannot use fix reax/bonds without pair_style reax} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Cannot use fix rigid npt/nph and fix deform on same component of stress tensor} :dt
 
@@ -2076,7 +2088,7 @@ Self-explanatory. :dd
 
 {Cannot use lines with fix srd unless overlap is set} :dt
 
-This is because line segements are connected to each other. :dd
+This is because line segments are connected to each other. :dd
 
 {Cannot use multiple fix wall commands with pair brownian} :dt
 
@@ -2119,7 +2131,7 @@ Self-explanatory. :dd
 
 {Cannot use newton pair with born/gpu pair style} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Cannot use newton pair with buck/coul/cut/gpu pair style} :dt
 
@@ -2279,7 +2291,7 @@ Self-explanatory. :dd
 
 {Cannot use newton pair with zbl/gpu pair style} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Cannot use non-zero forces in an energy minimization} :dt
 
@@ -2629,11 +2641,11 @@ uses a pairwise neighbor list. :dd
 
 {Compute chunk/atom bin/cylinder radius is too large for periodic box} :dt
 
-Radius cannot be bigger than 1/2 of a non-axis  periodic dimention. :dd
+Radius cannot be bigger than 1/2 of a non-axis  periodic dimension. :dd
 
 {Compute chunk/atom bin/sphere radius is too large for periodic box} :dt
 
-Radius cannot be bigger than 1/2 of any periodic dimention. :dd
+Radius cannot be bigger than 1/2 of any periodic dimension. :dd
 
 {Compute chunk/atom compute array is accessed out-of-range} :dt
 
@@ -2694,15 +2706,15 @@ It will only store IDs if its compress option is enabled. :dd
 
 {Compute chunk/atom stores no coord1 for compute property/chunk} :dt
 
-Only certain binning options for comptue chunk/atom store coordinates. :dd
+Only certain binning options for compute chunk/atom store coordinates. :dd
 
 {Compute chunk/atom stores no coord2 for compute property/chunk} :dt
 
-Only certain binning options for comptue chunk/atom store coordinates. :dd
+Only certain binning options for compute chunk/atom store coordinates. :dd
 
 {Compute chunk/atom stores no coord3 for compute property/chunk} :dt
 
-Only certain binning options for comptue chunk/atom store coordinates. :dd
+Only certain binning options for compute chunk/atom store coordinates. :dd
 
 {Compute chunk/atom variable is not atom-style variable} :dt
 
@@ -2723,11 +2735,11 @@ is used to find clusters. :dd
 
 {Compute cna/atom cutoff is longer than pairwise cutoff} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Compute cna/atom requires a pair style be defined} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Compute com/chunk does not use chunk/atom compute} :dt
 
@@ -2735,7 +2747,7 @@ The style of the specified compute is not chunk/atom. :dd
 
 {Compute contact/atom requires a pair style be defined} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Compute contact/atom requires atom style sphere} :dt
 
@@ -2748,7 +2760,7 @@ since those atoms are not in the neighbor list. :dd
 
 {Compute coord/atom requires a pair style be defined} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Compute damage/atom requires peridynamic potential} :dt
 
@@ -2778,7 +2790,7 @@ Self-explanatory. :dd
 
 {Compute erotate/asphere requires extended particles} :dt
 
-This compute cannot be used with point paritlces. :dd
+This compute cannot be used with point particles. :dd
 
 {Compute erotate/rigid with non-rigid fix-ID} :dt
 
@@ -2823,7 +2835,7 @@ Cannot compute order parameter beyond cutoff. :dd
 
 {Compute hexorder/atom requires a pair style be defined} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Compute improper/local used when impropers are not allowed} :dt
 
@@ -2869,11 +2881,11 @@ Cannot compute order parameter beyond cutoff. :dd
 
 {Compute orientorder/atom requires a pair style be defined} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Compute pair must use group all} :dt
 
-Pair styles accumlate energy on all atoms. :dd
+Pair styles accumulate energy on all atoms. :dd
 
 {Compute pe must use group all} :dt
 
@@ -2923,7 +2935,7 @@ The style of the specified compute is not chunk/atom. :dd
 {Compute property/local cannot use these inputs together} :dt
 
 Only inputs that generate the same number of datums can be used
-togther.  E.g. bond and angle quantities cannot be mixed. :dd
+together.  E.g. bond and angle quantities cannot be mixed. :dd
 
 {Compute property/local does not (yet) work with atom_style template} :dt
 
@@ -3067,7 +3079,7 @@ Self-explanatory. :dd
 
 {Compute temp/asphere requires extended particles} :dt
 
-This compute cannot be used with point paritlces. :dd
+This compute cannot be used with point particles. :dd
 
 {Compute temp/body requires atom style body} :dt
 
@@ -3512,12 +3524,12 @@ path and name are correct. :dd
 
 {Could not process Python file} :dt
 
-The Python code in the specified file was not run sucessfully by
+The Python code in the specified file was not run successfully by
 Python, probably due to errors in the Python code. :dd
 
 {Could not process Python string} :dt
 
-The Python code in the here string was not run sucessfully by Python,
+The Python code in the here string was not run successfully by Python,
 probably due to errors in the Python code. :dd
 
 {Coulomb PPPMDisp order has been reduced below minorder} :dt
@@ -3626,7 +3638,7 @@ Self-explanatory. :dd
 
 {Cutoffs missing in pair_style buck/long/coul/long} :dt
 
-Self-exlanatory. :dd
+Self-explanatory. :dd
 
 {Cutoffs missing in pair_style lj/long/coul/long} :dt
 
@@ -4373,7 +4385,7 @@ Self-explanatory. :dd
 
 {Fix ave/chunk does not use chunk/atom compute} :dt
 
-The specified conpute is not for a compute chunk/atom command. :dd
+The specified compute is not for a compute chunk/atom command. :dd
 
 {Fix ave/chunk fix does not calculate a per-atom array} :dt
 
@@ -4605,11 +4617,11 @@ An index for the array is out of bounds. :dd
 
 {Fix ave/time compute does not calculate a scalar} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Fix ave/time compute does not calculate a vector} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Fix ave/time compute does not calculate an array} :dt
 
@@ -4958,7 +4970,7 @@ Self-explanatory. :dd
 
 {Fix langevin angmom requires extended particles} :dt
 
-This fix option cannot be used with point paritlces. :dd
+This fix option cannot be used with point particles. :dd
 
 {Fix langevin omega is not yet implemented with kokkos} :dt
 
@@ -6159,7 +6171,7 @@ map command will force an atom map to be created. :dd
 
 {Initial temperatures not all set in fix ttm} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Input line quote not followed by whitespace} :dt
 
@@ -6187,7 +6199,7 @@ Eigensolve for rigid body was not sufficiently accurate. :dd
 
 {Insufficient Jacobi rotations for triangle} :dt
 
-The calculation of the intertia tensor of the triangle failed.  This
+The calculation of the inertia tensor of the triangle failed.  This
 should not happen if it is a reasonably shaped triangle. :dd
 
 {Insufficient memory on accelerator} :dt
@@ -6451,15 +6463,15 @@ Self-explanatory. :dd
 
 {Invalid attribute in dump custom command} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Invalid attribute in dump local command} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Invalid attribute in dump modify command} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Invalid basis setting in create_atoms command} :dt
 
@@ -6725,7 +6737,7 @@ or cause multiple files to be written. :dd
 Filenames used with the dump xyz style cannot be binary or cause files
 to be written by each processor. :dd
 
-{Invalid dump_modify threshhold operator} :dt
+{Invalid dump_modify threshold operator} :dt
 
 Operator keyword used for threshold specification in not recognized. :dd
 
@@ -6739,7 +6751,7 @@ The fix is not recognized. :dd
 
 {Invalid fix ave/time off column} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Invalid fix box/relax command for a 2d simulation} :dt
 
@@ -7301,7 +7313,7 @@ Self-explanatory. Check the input script or data file. :dd
 
 {LJ6 off not supported in pair_style buck/long/coul/long} :dt
 
-Self-exlanatory. :dd
+Self-explanatory. :dd
 
 {Label wasn't found in input script} :dt
 
@@ -7349,7 +7361,7 @@ This should not occur.  Report the problem to the developers. :dd
 Lost atoms are checked for each time thermo output is done.  See the
 thermo_modify lost command for options.  Lost atoms usually indicate
 bad dynamics, e.g. atoms have been blown far out of the simulation
-box, or moved futher than one processor's sub-domain away before
+box, or moved further than one processor's sub-domain away before
 reneighboring. :dd
 
 {MEAM library error %d} :dt
@@ -7514,7 +7526,7 @@ Self-explanatory. :dd
 
 {Molecule template ID for create_atoms does not exist} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Molecule template ID for fix deposit does not exist} :dt
 
@@ -7540,7 +7552,7 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Molecule toplogy/atom exceeds system topology/atom} :dt
+{Molecule topology/atom exceeds system topology/atom} :dt
 
 The number of bonds, angles, etc per-atom in the molecule exceeds the
 system setting.  See the create_box command for how to specify these
@@ -7780,7 +7792,7 @@ Self-explanatory. :dd
 
 {Must use variable energy with fix addforce} :dt
 
-Must define an energy vartiable when applyting a dynamic
+Must define an energy variable when applying a dynamic
 force during minimization. :dd
 
 {Must use variable energy with fix efield} :dt
@@ -8030,7 +8042,7 @@ Self-explanatory. :dd
 
 {Non digit character between brackets in variable} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Non integer # of swaps in temper command} :dt
 
@@ -8651,7 +8663,7 @@ not be invoked by bond_style quartic. :dd
 {Pair style does not support compute group/group} :dt
 
 The pair_style does not have a single() function, so it cannot be
-invokded by the compute group/group command. :dd
+invoked by the compute group/group command. :dd
 
 {Pair style does not support compute pair/local} :dt
 
@@ -8936,11 +8948,11 @@ Self-explanatory. :dd
 
 {Pair yukawa/colloid requires atom style sphere} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Pair yukawa/colloid requires atoms with same type have same radius} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Pair yukawa/colloid/gpu requires atom style sphere} :dt
 
@@ -9154,7 +9166,7 @@ Self-explanatory. :dd
 
 {Python function evaluation failed} :dt
 
-The Python function did not run succesfully and/or did not return a
+The Python function did not run successfully and/or did not return a
 value (if it is supposed to return a value).  This is probably due to
 some error condition in the function. :dd
 
@@ -10013,7 +10025,7 @@ make sense in between runs. :dd
 
 {Threshhold for an atom property that isn't allocated} :dt
 
-A dump threshhold has been requested on a quantity that is
+A dump threshold has been requested on a quantity that is
 not defined by the atom style used in this simulation. :dd
 
 {Timestep must be >= 0} :dt
@@ -10075,7 +10087,7 @@ to a large size. :dd
 {Too many atom triplets for pair bop} :dt
 
 The number of three atom groups for angle determinations exceeds the
-expected number.  Check your atomic structrure to ensure that it is
+expected number.  Check your atomic structure to ensure that it is
 realistic. :dd
 
 {Too many atoms for dump dcd} :dt
@@ -10143,7 +10155,7 @@ to a large size. :dd
 
 {Too many timesteps} :dt
 
-The cummulative timesteps must fit in a 64-bit integer. :dd
+The cumulative timesteps must fit in a 64-bit integer. :dd
 
 {Too many timesteps for NEB} :dt
 
@@ -10642,7 +10654,7 @@ Only atom-style variables can be used. :dd
 
 {Variable for region cylinder is invalid style} :dt
 
-Only equal-style varaibles are allowed. :dd
+Only equal-style variables are allowed. :dd
 
 {Variable for region is invalid style} :dt
 
@@ -10654,7 +10666,7 @@ Self-explanatory. :dd
 
 {Variable for region sphere is invalid style} :dt
 
-Only equal-style varaibles are allowed. :dd
+Only equal-style variables are allowed. :dd
 
 {Variable for restart is invalid style} :dt
 
@@ -10695,7 +10707,7 @@ Self-explanatory. :dd
 {Variable has circular dependency} :dt
 
 A circular dependency is when variable "a" in used by variable "b" and
-variable "b" is also used by varaible "a".  Circular dependencies with
+variable "b" is also used by variable "a".  Circular dependencies with
 longer chains of dependence are also not allowed. :dd
 
 {Variable name between brackets must be alphanumeric or underscore characters} :dt
@@ -10784,7 +10796,7 @@ Self-explanatory. :dd
 
 {Variable name for fix deform does not exist} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Variable name for fix efield does not exist} :dt
 
@@ -11071,7 +11083,7 @@ for a dihedral) and adding a small amount of stretch. :dd
 
 {Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt
 
-Self-explantory. :dd
+Self-explanatory. :dd
 
 {Calling write_dump before a full system init.} :dt
 
@@ -11159,6 +11171,12 @@ Self-explanatory. :dd
 If the fix changes the timestep, the dump dcd file will not
 reflect the change. :dd
 
+{Energy due to X extra global DOFs will be included in minimizer energies} :dt
+
+When using fixes like box/relax, the potential energy used by the minimizer
+is augmented by an additional energy provided by the fix. Thus the printed
+converged energy may be different from the total potential energy. :dd
+
 {Energy tally does not account for 'zero yes'} :dt
 
 The energy removed by using the 'zero yes' flag is not accounted
@@ -11402,7 +11420,7 @@ The command options you have used caused atoms to be lost. :dd
 Lost atoms are checked for each time thermo output is done.  See the
 thermo_modify lost command for options.  Lost atoms usually indicate
 bad dynamics, e.g. atoms have been blown far out of the simulation
-box, or moved futher than one processor's sub-domain away before
+box, or moved further than one processor's sub-domain away before
 reneighboring. :dd
 
 {MSM mesh too small, increasing to 2 points in each direction} :dt
@@ -11440,7 +11458,7 @@ i.e. the first molecule in the template. :dd
 
 {Molecule template for fix shake has multiple molecules} :dt
 
-The fix shake command will only recoginze molecules of a single
+The fix shake command will only recognize molecules of a single
 type, i.e. the first molecule in the template. :dd
 
 {More than one compute centro/atom} :dt
@@ -11525,7 +11543,7 @@ neigh_modify exclude command. :dd
 
 If a thermo_style command is used after a thermo_modify command, the
 settings changed by the thermo_modify command will be reset to their
-default values.  This is because the thermo_modify commmand acts on
+default values.  This is because the thermo_modify command acts on
 the currently defined thermo style, and a thermo_style command creates
 a new style. :dd
 
@@ -11577,7 +11595,7 @@ This may not be what you intended. :dd
 
 {One or more dynamic groups may not be updated at correct point in timestep} :dt
 
-If there are other fixes that act immediately after the intitial stage
+If there are other fixes that act immediately after the initial stage
 of time integration within a timestep (i.e. after atoms move), then
 the command that sets up the dynamic group should appear after those
 fixes.  This will insure that dynamic group assignments are made
@@ -11874,7 +11892,7 @@ Self-explanatory. :dd
 
 {Using largest cutoff for buck/long/coul/long} :dt
 
-Self-exlanatory. :dd
+Self-explanatory. :dd
 
 {Using largest cutoff for lj/long/coul/long} :dt
 

doc/src/Section_example.txt

@@ -25,9 +25,7 @@ files and image files.
 
 If you uncomment the "dump"_dump.html command in the input script, a
 text dump file will be produced, which can be animated by various
-"visualization programs"_http://lammps.sandia.gov/viz.html.  It can
-also be animated using the xmovie tool described in the "Additional
-Tools"_Section_tools.html section of the LAMMPS documentation.
+"visualization programs"_http://lammps.sandia.gov/viz.html.
 
 If you uncomment the "dump image"_dump.html command in the input
 script, and assuming you have built LAMMPS with a JPG library, JPG
@@ -53,9 +51,11 @@ Lowercase directories :h4
 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
+cmap:     CMAP 5-body contributions to CHARMM force field
 colloid:  big colloid particles in a small particle solvent, 2d system
 comb:     models using the COMB potential
 coreshell: core/shell model using CORESHELL package
+controller: use of fix controller as a thermostat
 crack:    crack propagation in a 2d solid
 deposit:  deposit atoms and molecules on a surface
 dipole:   point dipolar particles, 2d system
@@ -64,6 +64,8 @@ eim:      NaCl using the EIM potential
 ellipse:  ellipsoidal particles in spherical solvent, 2d system
 flow:     Couette and Poiseuille flow in a 2d channel
 friction: frictional contact of spherical asperities between 2d surfaces
+gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
+granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
 indent:   spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
@@ -71,6 +73,7 @@ meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:      energy minimization of 2d LJ melt
+mscg:     parameterize a multi-scale coarse-graining (MSCG) model
 msst:     MSST shock dynamics
 nb3b:     use of nonbonded 3-body harmonic pair style
 neb:      nudged elastic band (NEB) calculation for barrier finding
@@ -89,7 +92,8 @@ snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
 srd:      stochastic rotation dynamics (SRD) particles as solvent
 streitz:  use of Streitz/Mintmire potential with charge equilibration
 tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
-vashishta: use of the Vashishta potential :tb(s=:)
+vashishta: use of the Vashishta potential
+voronoi:  Voronoi tesselation via compute voronoi/atom command :tb(s=:)
 
 Here is how you can run and visualize one of the sample problems:
 

doc/src/Section_history.txt

@@ -37,7 +37,7 @@ pitfalls or alternatives.
 
 Please see some of the closed issues for examples of how to
 suggest code enhancements, submit proposed changes, or report
-possible bugs and how they are resoved.
+possible bugs and how they are resolved.
 
 As an alternative to using GitHub, you may e-mail the
 "core developers"_http://lammps.sandia.gov/authors.html or send

doc/src/Section_howto.txt

@@ -165,9 +165,16 @@ Many of the example input scripts included in the LAMMPS distribution
 are for 2d models.
 
 NOTE: Some models in LAMMPS treat particles as finite-size spheres, as
-opposed to point particles.  In 2d, the particles will still be
-spheres, not disks, meaning their moment of inertia will be the same
-as in 3d.
+opposed to point particles.  See the "atom_style
+sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html
+commands for details.  By default, for 2d simulations, such particles
+will still be modeled as 3d spheres, not 2d discs (circles), meaning
+their moment of inertia will be that of a sphere.  If you wish to
+model them as 2d discs, see the "set density/disc"_set.html command
+and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html,
+"fix nvt/sphere"_fix_nvt_sphere.html, "fix
+nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html
+commands.
 
 :line
 
@@ -197,7 +204,10 @@ documentation for the formula it computes.
 
 "bond_style"_bond_harmonic.html harmonic
 "angle_style"_angle_charmm.html charmm
+"dihedral_style"_dihedral_charmm.html charmmfsh
 "dihedral_style"_dihedral_charmm.html charmm
+"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh
+"pair_style"_pair_charmm.html lj/charmmfsw/coul/long
 "pair_style"_pair_charmm.html lj/charmm/coul/charmm
 "pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
 "pair_style"_pair_charmm.html lj/charmm/coul/long :ul
@@ -205,6 +215,12 @@ documentation for the formula it computes.
 "special_bonds"_special_bonds.html charmm
 "special_bonds"_special_bonds.html amber :ul
 
+NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
+released in March 2017.  We recommend they be used instead of the
+older {charmm} styles.  See discussion of the differences on the "pair
+charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
+doc pages.
+
 DREIDING is a generic force field developed by the "Goddard
 group"_http://www.wag.caltech.edu at Caltech and is useful for
 predicting structures and dynamics of organic, biological and
@@ -434,6 +450,12 @@ computations between frozen atoms by using this command:
 
 "neigh_modify"_neigh_modify.html exclude :ul
 
+NOTE: By default, for 2d systems, granular particles are still modeled
+as 3d spheres, not 2d discs (circles), meaning their moment of inertia
+will be the same as in 3d.  If you wish to model granular particles in
+2d as 2d discs, see the note on this topic in "Section
+6.2"_Section_howto.html#howto_2, where 2d simulations are disussed.
+
 :line
 
 6.7 TIP3P water model :link(howto_7),h4
@@ -451,7 +473,7 @@ atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
 cutoff.  The K values can be used if a flexible TIP3P model (without
 fix shake) is desired.  If the LJ epsilon and sigma for HH and OH are
 set to 0.0, it corresponds to the original 1983 TIP3P model
-"(Jorgensen)"_#Jorgensen.
+"(Jorgensen)"_#Jorgensen1.
 
 O mass = 15.9994
 H mass = 1.008
@@ -469,7 +491,7 @@ K of HOH angle = 55
 theta of HOH angle = 104.52 :all(b),p
 
 These are the parameters to use for TIP3P with a long-range Coulombic
-solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price for
+solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for
 details:
 
 O mass = 15.9994
@@ -513,7 +535,7 @@ using the "fix shake"_fix_shake.html command.
 
 These are the additional parameters (in real units) to set for O and H
 atoms and the water molecule to run a rigid TIP4P model with a cutoff
-"(Jorgensen)"_#Jorgensen.  Note that the OM distance is specified in
+"(Jorgensen)"_#Jorgensen1.  Note that the OM distance is specified in
 the "pair_style"_pair_style.html command, not as part of the pair
 coefficients.
 
@@ -573,7 +595,7 @@ LJ epsilon of O-O = 0.16275
 LJ sigma of O-O = 3.16435
 LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
 
-Note that the when using the TIP4P pair style, the neighobr list
+Note that the when using the TIP4P pair style, the neighbor list
 cutoff for Coulomb interactions is effectively extended by a distance
 2 * (OM distance), to account for the offset distance of the
 fictitious charges on O atoms in water molecules.  Thus it is
@@ -618,7 +640,7 @@ any of the parameters above, though it becomes a different model in
 that mode of usage.
 
 The SPC/E (extended) water model is the same, except
-the partial charge assignemnts change:
+the partial charge assignments change:
 
 O charge = -0.8476
 H charge = 0.4238 :all(b),p
@@ -737,23 +759,14 @@ LAMMPS itself does not do visualization, but snapshots from LAMMPS
 simulations can be visualized (and analyzed) in a variety of ways.
 
 LAMMPS snapshots are created by the "dump"_dump.html command which can
-create files in several formats.  The native LAMMPS dump format is a
+create files in several formats. The native LAMMPS dump format is a
 text file (see "dump atom" or "dump custom") which can be visualized
-by the "xmovie"_Section_tools.html#xmovie program, included with the
-LAMMPS package.  This produces simple, fast 2d projections of 3d
-systems, and can be useful for rapid debugging of simulation geometry
-and atom trajectories.
-
+by several popular visualization tools. The "dump image"_dump_image.html
+and "dump movie"_dump_image.html styles can output internally rendered
+images and convert a sequence of them to a movie during the MD run.
 Several programs included with LAMMPS as auxiliary tools can convert
-native LAMMPS dump files to other formats.  See the
-"Section 9"_Section_tools.html doc page for details.  The first is
-the "ch2lmp tool"_Section_tools.html#charmm, which contains a
-lammps2pdb Perl script which converts LAMMPS dump files into PDB
-files.  The second is the "lmp2arc tool"_Section_tools.html#arc which
-converts LAMMPS dump files into Accelrys' Insight MD program files.
-The third is the "lmp2cfg tool"_Section_tools.html#cfg which converts
-LAMMPS dump files into CFG files which can be read into the
-"AtomEye"_atomeye visualizer.
+between LAMMPS format files and other formats.
+See the "Section 9"_Section_tools.html doc page for details.
 
 A Python-based toolkit distributed by our group can read native LAMMPS
 dump files, including custom dump files with additional columns of
@@ -766,22 +779,7 @@ RasMol visualization programs.  Pizza.py has tools that do interactive
 3d OpenGL visualization and one that creates SVG images of dump file
 snapshots.
 
-LAMMPS can create XYZ files directly (via "dump xyz") which is a
-simple text-based file format used by many visualization programs
-including "VMD"_vmd.
-
-LAMMPS can create DCD files directly (via "dump dcd") which can be
-read by "VMD"_vmd in conjunction with a CHARMM PSF file.  Using this
-form of output avoids the need to convert LAMMPS snapshots to PDB
-files.  See the "dump"_dump.html command for more information on DCD
-files.
-
-LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
-file format which can also be read by "VMD"_vmd for visualization.
-See the "dump"_dump.html command for more information on XTC files.
-
 :link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
-:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
 :link(ensight,http://www.ensight.com)
 :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
 
@@ -863,7 +861,7 @@ boundary conditions in specific dimensions.  See the command doc pages
 for details.
 
 The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
-time the simluation box is created.  This happens in one of 3 ways.
+time the simulation box is created.  This happens in one of 3 ways.
 If the "create_box"_create_box.html command is used with a region of
 style {prism}, then a triclinic box is setup.  See the
 "region"_region.html command for details.  If the
@@ -982,10 +980,10 @@ used with non-orthogonal basis vectors to define a lattice that will
 tile a triclinic simulation box via the
 "create_atoms"_create_atoms.html command.
 
-A second use is to run Parinello-Rahman dyanamics via the "fix
+A second use is to run Parinello-Rahman dynamics via the "fix
 npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
 factors to compensate for off-diagonal components of the pressure
-tensor.  The analalog for an "energy minimization"_minimize.html is
+tensor.  The analog for an "energy minimization"_minimize.html is
 the "fix box/relax"_fix_box_relax.html command.
 
 A third use is to shear a bulk solid to study the response of the
@@ -1032,6 +1030,10 @@ profile consistent with the applied shear strain rate.
 An alternative method for calculating viscosities is provided via the
 "fix viscosity"_fix_viscosity.html command.
 
+NEMD simulations can also be used to measure transport properties of a fluid
+through a pore or channel. Simulations of steady-state flow can be performed
+using the "fix flow/gauss"_fix_flow_gauss.html command.
+
 :line
 
 6.14 Finite-size spherical and aspherical particles :link(howto_14),h4
@@ -1392,7 +1394,7 @@ custom"_dump.html command.
 
 There is also a "dump local"_dump.html format where the user specifies
 what local values to output.  A pre-defined index keyword can be
-specified to enumuerate the local values.  Two additional kinds of
+specified to enumerate the local values.  Two additional kinds of
 keywords can also be specified (c_ID, f_ID), where a
 "compute"_compute.html or "fix"_fix.html or "variable"_variable.html
 provides the values to be output.  In each case, the compute or fix
@@ -1525,7 +1527,7 @@ Variables that generate values to output :h5,link(variable)
 "Variables"_variable.html defined in an input script can store one or
 more strings.  But equal-style, vector-style, and atom-style or
 atomfile-style variables generate a global scalar value, global vector
-or values, or a per-atom vector, resepctively, when accessed.  The
+or values, or a per-atom vector, respectively, when accessed.  The
 formulas used to define these variables can contain references to the
 thermodynamic keywords and to global and per-atom data generated by
 computes, fixes, and other variables.  The values generated by
@@ -1585,7 +1587,7 @@ Temperature is computed as kinetic energy divided by some number of
 degrees of freedom (and the Boltzmann constant).  Since kinetic energy
 is a function of particle velocity, there is often a need to
 distinguish between a particle's advection velocity (due to some
-aggregate motiion of particles) and its thermal velocity.  The sum of
+aggregate motion of particles) and its thermal velocity.  The sum of
 the two is the particle's total velocity, but the latter is often what
 is wanted to compute a temperature.
 
@@ -1640,14 +1642,14 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
 velocities but also rotational velocities for spherical and aspherical
 particles.
 
-DPD thermostatting alters pairwise interactions in a manner analagous
+DPD thermostatting alters pairwise interactions in a manner analogous
 to the per-particle thermostatting of "fix
 langevin"_fix_langevin.html.
 
 Any of the thermostatting fixes can use temperature computes that
 remove bias which has two effects.  First, the current calculated
 temperature, which is compared to the requested target temperature, is
-caluclated with the velocity bias removed.  Second, the thermostat
+calculated with the velocity bias removed.  Second, the thermostat
 adjusts only the thermal temperature component of the particle's
 velocities, which are the velocities with the bias removed.  The
 removed bias is then added back to the adjusted velocities.  See the
@@ -1684,7 +1686,7 @@ nph) and Berendsen:
 The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
 and barostat.  "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
 it does no thermostatting.  Both "fix nph"_fix_nh.html and "fix
-press/bernendsen"_fix_press_berendsen.html can be used in conjunction
+press/berendsen"_fix_press_berendsen.html can be used in conjunction
 with any of the thermostatting fixes.
 
 As with the thermostats, "fix npt"_fix_nh.html and "fix
@@ -1834,7 +1836,7 @@ the deformation must be chosen judiciously, and care must be taken to
 fully equilibrate the deformed cell before sampling the stress
 tensor. Another approach is to sample the triclinic cell fluctuations
 that occur in an NPT simulation. This method can also be slow to
-converge and requires careful post-processing "(Shinoda)"_#Shinoda
+converge and requires careful post-processing "(Shinoda)"_#Shinoda1
 
 :line
 
@@ -1888,7 +1890,7 @@ 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.
+used to instantiate LAMMPS, and MPI is initialized if necessary.
 
 The lammps_close() function is used to shut down an instance of LAMMPS
 and free all its memory.
@@ -1957,9 +1959,12 @@ 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 extract_atom() method, see the extract() method in the
+src/atom.cpp file for a list of valid per-atom properties.  New names
+could easily be added if the property you want is not listed.  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_reset_box() function resets the size and shape of the
 simulation box, e.g. as part of restoring a previously extracted and
@@ -1975,11 +1980,20 @@ keyword as a double precision value.
 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
 lammps_gather_atoms() and lammps_scatter_atoms() functions.  The
-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, 
+gather function collects peratom info of the requested type (atom
+coords, types, forces, etc) from all processors, orders them by atom
+ID, and returns a full list to each calling processor.  The scatter
+function does the inverse.  It distributes the same peratom values,
 passed by the caller, to each atom owned by individual processors.
+Both methods are thus a means to extract or assign (overwrite) any
+peratom quantities within LAMMPS.  See the extract() method in the
+src/atom.cpp file for a list of valid per-atom properties.  New names
+could easily be added if the property you want is not listed.
+A special treatment is applied for accessing image flags via the
+"image" property. Image flags are stored in a packed format with all
+three image flags stored in a single integer. When signaling to access
+the image flags as 3 individual values per atom instead of 1, the data
+is transparently packed or unpacked by the library interface.
 
 The lammps_create_atoms() function takes a list of N atoms as input
 with atom types and coords (required), an optionally atom IDs and
@@ -2013,7 +2027,7 @@ a simple Lennard-Jones fluid model.  Also, see "this
 section"_Section_howto.html#howto_21 of the manual for an analogous
 discussion for viscosity.
 
-The thermal conducitivity tensor kappa is a measure of the propensity
+The thermal conductivity tensor kappa is a measure of the propensity
 of a material to transmit heat energy in a diffusive manner as given
 by Fourier's law
 
@@ -2099,7 +2113,7 @@ and grad(Vstream) is the spatial gradient of the velocity of the fluid
 moving in another direction, normal to the area through which the
 momentum flows.  Viscosity thus has units of pressure-time.
 
-The first method is to perform a non-equlibrium MD (NEMD) simulation
+The first method is to perform a non-equilibrium MD (NEMD) simulation
 by shearing the simulation box via the "fix deform"_fix_deform.html
 command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to
 thermostat the fluid via the SLLOD equations of motion.
@@ -2125,7 +2139,7 @@ the rNEMD algorithm of Muller-Plathe.  Momentum in one dimension is
 swapped between atoms in two different layers of the simulation box in
 a different dimension.  This induces a velocity gradient which can be
 monitored with the "fix ave/chunk"_fix_ave_chunk.html command.
-The fix tallies the cummulative momentum transfer that it performs.
+The fix tallies the cumulative momentum transfer that it performs.
 See the "fix viscosity"_fix_viscosity.html command for details.
 
 The fourth method is based on the Green-Kubo (GK) formula which
@@ -2268,7 +2282,7 @@ atoms with same local defect structure | chunk ID = output of "compute centro/at
 Note that chunk IDs are integer values, so for atom properties or
 computes that produce a floating point value, they will be truncated
 to an integer.  You could also use the compute in a variable that
-scales the floating point value to spread it across multiple intergers.
+scales the floating point value to spread it across multiple integers.
 
 Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
 pencils, 3d bins = boxes, spherical bins, cylindrical bins.
@@ -2353,7 +2367,7 @@ largest cluster or fastest diffusing molecule. :l
 
 Example calculations with chunks :h5
 
-Here are eaxmples using chunk commands to calculate various
+Here are examples using chunk commands to calculate various
 properties:
 
 (1) Average velocity in each of 1000 2d spatial bins:
@@ -2424,7 +2438,7 @@ which both have their up- and downsides.
 The first approach is to set desired real-space an kspace accuracies
 via the {kspace_modify force/disp/real} and {kspace_modify
 force/disp/kspace} commands. Note that the accuracies have to be
-specified in force units and are thus dependend on the chosen unit
+specified in force units and are thus dependent on the chosen unit
 settings. For real units, 0.0001 and 0.002 seem to provide reasonable
 accurate and efficient computations for the real-space and kspace
 accuracies.  0.002 and 0.05 work well for most systems using lj
@@ -2444,7 +2458,7 @@ performance. This approach provides a fast initialization of the
 simulation. However, it is sensitive to errors: A combination of
 parameters that will perform well for one system might result in
 far-from-optimal conditions for other simulations. For example,
-parametes that provide accurate and fast computations for
+parameters that provide accurate and fast computations for
 all-atomistic force fields can provide insufficient accuracy or
 united-atomistic force fields (which is related to that the latter
 typically have larger dispersion coefficients).
@@ -2478,7 +2492,7 @@ arithmetic mixing rule substantially increases the computational cost.
 The computational overhead can be reduced using the {kspace_modify
 mix/disp geom} and {kspace_modify splittol} commands. The first
 command simply enforces geometric mixing of the dispersion
-coeffiecients in kspace computations.  This introduces some error in
+coefficients in kspace computations.  This introduces some error in
 the computations but will also significantly speed-up the
 simulations. The second keyword sets the accuracy with which the
 dispersion coefficients are approximated using a matrix factorization
@@ -2497,7 +2511,7 @@ to specify this command explicitly.
 6.25 Polarizable models :link(howto_25),h4
 
 In polarizable force fields the charge distributions in molecules and
-materials respond to their electrostatic environements. Polarizable
+materials respond to their electrostatic environments. Polarizable
 systems can be simulated in LAMMPS using three methods:
 
 the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html
@@ -2551,7 +2565,7 @@ this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
 charge-on-spring models by the methods outlined in the next two
 sections. The assignment of masses to the additional degrees of
 freedom can lead to unphysical trajectories if care is not exerted in
-choosing the parameters of the poarizable models and the simulation
+choosing the parameters of the polarizable models and the simulation
 conditions.
 
 In the core-shell model the vibration of the shells is kept faster
@@ -2573,7 +2587,7 @@ well.
 6.26 Adiabatic core/shell model :link(howto_26),h4
 
 The adiabatic core-shell model by "Mitchell and
-Finchham"_#MitchellFinchham is a simple method for adding
+Fincham"_#MitchellFincham is a simple method for adding
 polarizability to a system.  In order to mimic the electron shell of
 an ion, a satellite particle is attached to it. This way the ions are
 split into a core and a shell where the latter is meant to react to
@@ -2667,13 +2681,16 @@ bond_coeff      1 63.014 0.0
 bond_coeff      2 25.724 0.0 :pre
 
 When running dynamics with the adiabatic core/shell model, the
-following issues should be considered.  Since the relative motion of
-the core and shell particles corresponds to the polarization, typical
-thermostats can alter the polarization behaviour, meaning the shell
-will not react freely to its electrostatic environment.  This is
-critical during the equilibration of the system. Therefore
-it's typically desirable to decouple the relative motion of the
-core/shell pair, which is an imaginary degree of freedom, from the
+following issues should be considered.  The relative motion of
+the core and shell particles corresponds to the polarization, 
+hereby an instantaneous relaxation of the shells is approximated 
+and a fast core/shell spring frequency ensures a nearly constant
+internal kinetic energy during the simulation. 
+Thermostats can alter this polarization behaviour, by scaling the
+internal kinetic energy, meaning the shell will not react freely to 
+its electrostatic environment. 
+Therefore it is typically desirable to decouple the relative motion of 
+the core/shell pair, which is an imaginary degree of freedom, from the
 real physical system.  To do that, the "compute
 temp/cs"_compute_temp_cs.html command can be used, in conjunction with
 any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
@@ -2704,44 +2721,54 @@ fix thermostatequ all nve                               # integrator as needed f
 fix_modify thermoberendsen temp CSequ
 thermo_modify temp CSequ                                # output of center-of-mass derived temperature :pre
 
+The pressure for the core/shell system is computed via the regular 
+LAMMPS convention by "treating the cores and shells as individual 
+particles"_#MitchellFincham2. For the thermo output of the pressure 
+as well as for the application of a barostat, it is necessary to 
+use an additional "pressure"_compute_pressure compute based on the 
+default "temperature"_compute_temp and specifying it as a second 
+argument in "fix modify"_fix_modify.html and 
+"thermo_modify"_thermo_modify.html resulting in:
+
+(...)
+compute CSequ all temp/cs cores shells
+compute thermo_press_lmp all pressure thermo_temp       # pressure for individual particles
+thermo_modify temp CSequ press thermo_press_lmp         # modify thermo to regular pressure
+fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
+fix_modify press_bar temp CSequ press thermo_press_lmp  # pressure modification for correct kinetic scalar :pre
+
 If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
 relative motion of the core and the shell should in theory be
 stable.  However numerical fluctuation can introduce a small
 momentum to the system, which is noticable over long trajectories.
-Therefore it is recomendable to use the "fix
+Therefore it is recommendable to use the "fix
 momentum"_fix_momentum.html command in combination with "compute
 temp/cs"_compute_temp_cs.html when equilibrating the system to
 prevent any drift.
 
-When intializing the velocities of a system with core/shell pairs, it
+When initializing the velocities of a system with core/shell pairs, it
 is also desirable to not introduce energy into the relative motion of
 the core/shell particles, but only assign a center-of-mass velocity to
 the pairs.  This can be done by using the {bias} keyword of the
 "velocity create"_velocity.html command and assigning the "compute
 temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
-"velocity"_velocity.html commmand, e.g.
+"velocity"_velocity.html command, e.g.
 
 velocity all create 1427 134 bias yes temp CSequ
 velocity all scale 1427 temp CSequ :pre
 
-It is important to note that the polarizability of the core/shell
-pairs is based on their relative motion. Therefore the choice of
-spring force and mass ratio need to ensure much faster relative motion
-of the 2 atoms within the core/shell pair than their center-of-mass
-velocity. This allow the shells to effectively react instantaneously
-to the electrostatic environment.  This fast movement also limits the
-timestep size that can be used.
+To maintain the correct polarizability of the core/shell pairs, the 
+kinetic energy of the internal motion shall remain nearly constant. 
+Therefore the choice of spring force and mass ratio need to ensure 
+much faster relative motion of the 2 atoms within the core/shell pair 
+than their center-of-mass velocity. This allows the shells to 
+effectively react instantaneously to the electrostatic environment and 
+limits energy transfer to or from the core/shell oscillators.
+This fast movement also dictates the timestep that can be used.
 
 The primary literature of the adiabatic core/shell model suggests that
 the fast relative motion of the core/shell pairs only allows negligible
-energy transfer to the environment. Therefore it is not intended to
-decouple the core/shell degree of freedom from the physical system
-during production runs. In other words, the "compute
-temp/cs"_compute_temp_cs.html command should not be used during
-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).
-
+energy transfer to the environment. 
 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
@@ -2761,14 +2788,20 @@ command, to use as input to the "compute
 chunk/atom"_compute_chunk_atom.html command to define the core/shell
 pairs as chunks.
 
-For example,
+For example if core/shell pairs are the only molecules:
+
+read_data NaCl_CS_x0.1_prop.data 
+compute prop all property/atom molecule
+compute cs_chunk all chunk/atom c_prop
+compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
+fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
+
+For example if core/shell pairs and other molecules are present:
 
 fix csinfo all property/atom i_CSID                       # property/atom command
 read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info  # atom property added in the data-file
 compute prop all property/atom i_CSID
-compute cs_chunk all chunk/atom c_prop
-compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
-fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
+(...) :pre
 
 The additional section in the date file would be formatted like this:
 
@@ -2789,7 +2822,7 @@ CS-Info         # header of additional section :pre
 6.27 Drude induced dipoles :link(howto_27),h4
 
 The thermalized Drude model, similarly to the "core-shell"_#howto_26
-model, representes induced dipoles by a pair of charges (the core atom
+model, represents induced dipoles by a pair of charges (the core atom
 and the Drude particle) connected by a harmonic spring. The Drude
 model has a number of features aimed at its use in molecular systems
 ("Lamoureux and Roux"_#howto-Lamoureux):
@@ -2880,19 +2913,23 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
 [(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
 (1990).
 
-:link(Jorgensen)
+:link(Jorgensen1)
 [(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
 Phys, 79, 926 (1983).
 
-:link(Price)
+:link(Price1)
 [(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004).
 
-:link(Shinoda)
+:link(Shinoda1)
 [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
 
-:link(MitchellFinchham)
-[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
+:link(MitchellFincham)
+[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter,
 5, 1031-1038 (1993).
 
+:link(MitchellFincham2)
+[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
+6, 393-404 (1994).
+
 :link(howto-Lamoureux)
 [(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

doc/src/Section_intro.txt

@@ -249,8 +249,12 @@ Pizza.py WWW site"_pizza. :l
 
 Specialized features :h5
 
-These are LAMMPS capabilities which you may not think of as typical
-molecular dynamics options:
+LAMMPS can be built with optional packages which implement a variety
+of additional capabilities.  An overview of all the packages is "given
+here"_Section_packages.html.
+
+These are some LAMMPS capabilities which you may not think of as
+typical classical molecular dynamics options:
 
 "static"_balance.html and "dynamic load-balancing"_fix_balance.html
 "generalized aspherical particles"_body.html
@@ -338,15 +342,13 @@ dynamics timestepping, particularly if the computations are not
 parallel, so it is often better to leave such analysis to
 post-processing codes.
 
-A very simple (yet fast) visualizer is provided with the LAMMPS
-package - see the "xmovie"_Section_tools.html#xmovie tool in "this
-section"_Section_tools.html.  It creates xyz projection views of
-atomic coordinates and animates them.  We find it very useful for
-debugging purposes.  For high-quality visualization we recommend the
+For high-quality visualization we recommend the
 following packages:
 
 "VMD"_http://www.ks.uiuc.edu/Research/vmd
 "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
+"OVITO"_http://www.ovito.org/
+"ParaView"_http://www.paraview.org/
 "PyMol"_http://www.pymol.org
 "Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
 "RasMol"_http://www.openrasmol.org :ul
@@ -517,7 +519,7 @@ the packages they have written are somewhat unique to LAMMPS and the
 code would not be as general-purpose as it is without their expertise
 and efforts.
 
-Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages
+Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK and USER-OMP packages
 Roy Pollock (LLNL), Ewald and PPPM solvers
 Mike Brown (ORNL), brownw at ornl.gov, GPU package
 Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential

doc/src/Section_modify.txt

@@ -159,17 +159,17 @@ pack_comm_vel: add velocity info to communication buffer (required)
 pack_comm_hybrid: store extra info unique to this atom style (optional)
 unpack_comm: retrieve an atom's info from the buffer (required)
 unpack_comm_vel: also retrieve velocity info (required)
-unpack_comm_hybrid: retreive extra info unique to this atom style (optional)
+unpack_comm_hybrid: retrieve extra info unique to this atom style (optional)
 pack_reverse: store an atom's info in a buffer communicating partial forces  (required)
 pack_reverse_hybrid: store extra info unique to this atom style (optional)
 unpack_reverse: retrieve an atom's info from the buffer (required)
-unpack_reverse_hybrid: retreive extra info unique to this atom style (optional)
+unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional)
 pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required)
 pack_border_vel: add velocity info to buffer (required)
 pack_border_hybrid: store extra info unique to this atom style (optional)
 unpack_border: retrieve an atom's info from the buffer (required)
 unpack_border_vel: also retrieve velocity info (required)
-unpack_border_hybrid: retreive extra info unique to this atom style (optional)
+unpack_border_hybrid: retrieve extra info unique to this atom style (optional)
 pack_exchange: store all an atom's info to migrate to another processor (required)
 unpack_exchange: retrieve an atom's info from the buffer (required)
 size_restart: number of restart quantities associated with proc's atoms (required)
@@ -369,7 +369,7 @@ pre_force_respa: same as pre_force, but for rRESPA (optional)
 post_force_respa: same as post_force, but for rRESPA (optional)
 final_integrate_respa: same as final_integrate, but for rRESPA (optional)
 min_pre_force: called after pair & molecular forces are computed in minimizer (optional)
-min_post_force: called after pair & molecular forces are computed and communicated in minmizer (optional)
+min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional)
 min_store: store extra data for linesearch based minimization on a LIFO stack (optional)
 min_pushstore: push the minimization LIFO stack one element down (optional)
 min_popstore: pop the minimization LIFO stack one element up (optional)
@@ -517,7 +517,7 @@ class.  See region.h for details.
 inside: determine whether a point is in the region
 surface_interior: determine if a point is within a cutoff distance inside of surc
 surface_exterior: determine if a point is within a cutoff distance outside of surf
-shape_update : change region shape if set by time-depedent variable :tb(s=:)
+shape_update : change region shape if set by time-dependent variable :tb(s=:)
 
 :line
 
@@ -601,16 +601,16 @@ Adding keywords for the "thermo_style custom"_thermo_style.html command
 "here"_Section_modify.html#mod_13 on this page.
 
 Adding a new math function of one or two arguments can be done by
-editing one section of the Variable::evaulate() method.  Search for
+editing one section of the Variable::evaluate() method.  Search for
 the word "customize" to find the appropriate location.
 
 Adding a new group function can be done by editing one section of the
-Variable::evaulate() method.  Search for the word "customize" to find
+Variable::evaluate() method.  Search for the word "customize" to find
 the appropriate location.  You may need to add a new method to the
 Group class as well (see the group.cpp file).
 
 Accessing a new atom-based vector can be done by editing one section
-of the Variable::evaulate() method.  Search for the word "customize"
+of the Variable::evaluate() method.  Search for the word "customize"
 to find the appropriate location.
 
 Adding new "compute styles"_compute.html (whose calculated values can
@@ -740,7 +740,7 @@ entry to add to the USER-MISC/README file in that dir, along with the
 contribute several individual features.  :l
 
 If you want your contribution to be added as a user-contribution and
-it is several related featues, it is probably best to make it a user
+it is several related features, it is probably best to make it a user
 package directory with a name like USER-FOO.  In addition to your new
 files, the directory should contain a README text file.  The README
 should contain your name and contact information and a brief
@@ -785,10 +785,10 @@ file for how to format the cite itself.  The "Restrictions" section of
 the doc page should indicate that your command is only available if
 LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
 See other user package doc files for examples of how to do this. The
-prerequiste for building the HTML format files are Python 3.x and
+prerequisite for building the HTML format files are Python 3.x and
 virtualenv, the requirement for generating the PDF format manual
 is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least
-"make html" and carefully inspect and proofread the resuling HTML format
+"make html" and carefully inspect and proofread the resulting HTML format
 doc page before submitting your code. :l
 
 For a new package (or even a single command) you should include one or

doc/src/Section_perf.txt

@@ -69,7 +69,7 @@ bench/in.lj input script.
 
 For all the benchmarks, a useful metric is the CPU cost per atom per
 timestep.  Since performance scales roughly linearly with problem size
-and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained
+and timesteps for all LAMMPS models (i.e. interatomic or coarse-grained
 potentials), the run time of any problem using the same model (atom
 style, force field, cutoff, etc) can then be estimated.
 

doc/src/Section_python.txt

@@ -97,7 +97,7 @@ current LAMMPS library interface and how to call them from Python.
 Section 11.8 gives some examples of coupling LAMMPS to other tools via
 Python.  For example, LAMMPS can easily be coupled to a GUI or other
 visualization tools that display graphs or animations in real time as
-LAMMPS runs.  Examples of such scripts are inlcluded in the python
+LAMMPS runs.  Examples of such scripts are included in the python
 directory.
 
 Two advantages of using Python to run LAMMPS are how concise the
@@ -177,7 +177,7 @@ of Python and your machine to successfully build LAMMPS.  See the
 lib/python/README file for more info.
 
 If you want to write Python code with callbacks to LAMMPS, then you
-must also follow the steps overviewed in the preceeding section (11.1)
+must also follow the steps overviewed in the preceding section (11.1)
 for running LAMMPS from Python.  I.e. you must build LAMMPS as a
 shared library and insure that Python can find the python/lammps.py
 file and the shared library.
@@ -325,7 +325,7 @@ sudo python setup.py install :pre
 Again, the "sudo" is only needed if required to copy PyPar files into
 your Python distribution's site-packages directory.
 
-If you have successully installed PyPar, you should be able to run
+If you have successfully installed PyPar, you should be able to run
 Python and type
 
 import pypar :pre
@@ -369,7 +369,7 @@ user privilege into the user local directory type
 
 python setup.py install --user :pre
 
-If you have successully installed mpi4py, you should be able to run
+If you have successfully installed mpi4py, you should be able to run
 Python and type
 
 from mpi4py import MPI :pre
@@ -594,10 +594,10 @@ flag = lmp.set_variable(name,value)       # set existing named string-style vari
 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
+data = lmp.gather_atoms(name,type,count)  # return per-atom property of all atoms gathered into data, ordered by atom ID
                                           # name = "x", "charge", "type", etc
                                           # count = # of per-atom values, 1 or 3, etc
-lmp.scatter_atoms(name,type,count,data)   # scatter atom attribute of all atoms from data, ordered by atom ID
+lmp.scatter_atoms(name,type,count,data)   # scatter per-atom property to all atoms from data, ordered by atom ID
                                           # name = "x", "charge", "type", etc
                                           # count = # of per-atom values, 1 or 3, etc :pre
 
@@ -610,7 +610,7 @@ lmp = lammps() :pre
 
 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.
+is used to make all subsequent calls to the LAMMPS library.
 
 Additional arguments to lammps() can be used to tell Python the name
 of the shared library to load or to pass arguments to the LAMMPS
@@ -656,13 +656,13 @@ argument.
 For extract_atom(), a pointer to internal LAMMPS atom-based data is
 returned, which you can use via normal Python subscripting.  See the
 extract() method in the src/atom.cpp file for a list of valid names.
-Again, new names could easily be added.  A pointer to a vector of
-doubles or integers, or a pointer to an array of doubles (double **)
-or integers (int **) is returned.  You need to specify the appropriate
-data type via the type argument.
+Again, new names could easily be added if the property you want is not
+listed.  A pointer to a vector of doubles or integers, or a pointer to
+an array of doubles (double **) or integers (int **) is returned.  You
+need to specify the appropriate data type via the type argument.
 
 For extract_compute() and extract_fix(), the global, per-atom, or
-local data calulated by the compute or fix can be accessed.  What is
+local data calculated by the compute or fix can be accessed.  What is
 returned depends on whether the compute or fix calculates a scalar or
 vector or array.  For a scalar, a single double value is returned.  If
 the compute or fix calculates a vector or array, a pointer to the
@@ -689,12 +689,21 @@ specified group.
 The get_natoms() method returns the total number of atoms in the
 simulation, as an int.
 
-The gather_atoms() method returns a ctypes vector of ints or doubles
-as specified by type, of length count*natoms, for the property of all
-the atoms in the simulation specified by name, ordered by count and
-then by atom ID.  The vector can be used via normal Python
-subscripting.  If atom IDs are not consecutively ordered within
-LAMMPS, a None is returned as indication of an error.
+The gather_atoms() method allows any per-atom property (coordinates,
+velocities, etc) to be extracted from LAMMPS.  It returns a ctypes
+vector of ints or doubles as specified by type, of length
+count*natoms, for the named property for all atoms in the simulation.
+The data is ordered by count and then by atom ID.  See the extract()
+method in the src/atom.cpp file for a list of valid names.  Again, new
+names could easily be added if the property you want is missing.  The
+vector can be used via normal Python subscripting.  If atom IDs are
+not consecutively ordered within LAMMPS, a None is returned as
+indication of an error. A special treatment is applied for image flags
+stored in the "image" property. All three image flags are stored in
+a packed format in a single integer, so count would be 1 to retrieve
+that integer, however also a count value of 3 can be used and then
+the image flags will be unpacked into 3 individual integers, ordered
+in a similar fashion as coordinates. 
 
 Note that the data structure gather_atoms("x") returns is different
 from the data structure returned by extract_atom("x") in four ways.
@@ -711,14 +720,22 @@ assigning a new values to the extract_atom() array.  To do this with
 the gather_atoms() vector, you need to change values in the vector,
 then invoke the scatter_atoms() method.
 
-The scatter_atoms() method takes a vector of ints or doubles as
-specified by type, of length count*natoms, for the property of all the
-atoms in the simulation specified by name, ordered by bount and then
-by atom ID.  It uses the vector of data to overwrite the corresponding
-properties for each atom inside LAMMPS.  This requires LAMMPS to have
-its "map" option enabled; see the "atom_modify"_atom_modify.html
-command for details.  If it is not, or if atom IDs are not
-consecutively ordered, no coordinates are reset.
+The scatter_atoms() method allows any per-atom property (coordinates,
+velocities, etc) to be inserted into LAMMPS, overwriting the current
+property.  It takes a vector of ints or doubles as specified by type,
+of length count*natoms, for the named property for all atoms in the
+simulation.  The data should be ordered by count and then by atom ID.
+See the extract() method in the src/atom.cpp file for a list of valid
+names.  Again, new names could easily be added if the property you
+want is missing.  It uses the vector of data to overwrite the
+corresponding properties for each atom inside LAMMPS.  This requires
+LAMMPS to have its "map" option enabled; see the
+"atom_modify"_atom_modify.html command for details.  If it is not, or
+if atom IDs are not consecutively ordered, no coordinates are reset.
+Similar as for gather_atoms() a special treatment is applied for image
+flags, which can be provided in packed (count = 1) or unpacked (count = 3)
+format and in the latter case, they will be packed before applied to
+atoms.
 
 The array of coordinates passed to scatter_atoms() must be a ctypes
 vector of ints or doubles, allocated and initialized something like
@@ -734,7 +751,7 @@ x\[2\] = z coord of atom with ID 1
 x\[3\] = x coord of atom with ID 2
 ...
 x\[n3-1\] = z coord of atom with ID natoms
-lmp.scatter_coords("x",1,3,x) :pre
+lmp.scatter_atoms("x",1,3,x) :pre
 
 Alternatively, you can just change values in the vector returned by
 gather_atoms("x",1,3), since it is a ctypes vector of doubles.
@@ -774,7 +791,7 @@ demo.py, invoke various LAMMPS library interface routines,
 simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
 split.py, same as simple.py but running in parallel on a subset of procs,
 gui.py, GUI go/stop/temperature-slider to control LAMMPS,
-plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
+plot.py, real-time temperature plot with GnuPlot via Pizza.py,
 viz_tool.py, real-time viz via some viz package,
 vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2)
 

doc/src/Section_start.txt

@@ -14,12 +14,11 @@ experienced users.
 2.1 "What's in the LAMMPS distribution"_#start_1
 2.2 "Making LAMMPS"_#start_2
 2.3 "Making LAMMPS with optional packages"_#start_3
-2.4 "Building LAMMPS via the Make.py script"_#start_4
-2.5 "Building LAMMPS as a library"_#start_5
-2.6 "Running LAMMPS"_#start_6
-2.7 "Command-line options"_#start_7
-2.8 "Screen output"_#start_8
-2.9 "Tips for users of previous versions"_#start_9 :all(b)
+2.5 "Building LAMMPS as a library"_#start_4
+2.6 "Running LAMMPS"_#start_5
+2.7 "Command-line options"_#start_6
+2.8 "Screen output"_#start_7
+2.9 "Tips for users of previous versions"_#start_8 :all(b)
 
 :line
 
@@ -96,7 +95,7 @@ make serial :pre
 Note that on a facility supercomputer, there are often "modules"
 loaded in your environment that provide the compilers and MPI you
 should use.  In this case, the "mpicxx" compile/link command in
-Makefile.mpi should just work by accessing those modules.
+Makefile.mpi should simply work by accessing those modules.
 
 It may be the case that one of the other Makefile.machine files in the
 src/MAKE sub-directories is a better match to your system (type "make"
@@ -107,33 +106,35 @@ make stampede :pre
 If any of these builds (with an existing Makefile.machine) works on
 your system, then you're done!
 
+If you need to install an optional package with a LAMMPS command you
+want to use, and the package does not depend on an extra library, you
+can simply type
+
+make name :pre
+
+before invoking (or re-invoking) the above steps.  "Name" is the
+lower-case name of the package, e.g. replica or user-misc.
+
 If you want to do one of the following:
 
-use optional LAMMPS features that require additional libraries
-use optional packages that require additional libraries
-use optional accelerator packages that require special compiler/linker settings
-run on a specialized platform that has its own compilers, settings, or other libs to use :ul
+use a LAMMPS command that requires an extra library (e.g. "dump image"_dump_image.html)
+build with a package that requires an extra library
+build with an accelerator package that requires special compiler/linker settings
+run on a machine that has its own compilers, settings, or libraries :ul
 
 then building LAMMPS is more complicated.  You may need to find where
-auxiliary libraries exist on your machine or install them if they
-don't.  You may need to build additional libraries that are part of
-the LAMMPS package, before building LAMMPS.  You may need to edit a
+extra libraries exist on your machine or install them if they don't.
+You may need to build extra libraries that are included in the LAMMPS
+distribution, before building LAMMPS itself.  You may need to edit a
 Makefile.machine file to make it compatible with your system.
 
-Note that there is a Make.py tool in the src directory that automates
-several of these steps, but you still have to know what you are doing.
-"Section 2.4"_#start_4 below describes the tool.  It is a convenient
-way to work with installing/un-installing various packages, the
-Makefile.machine changes required by some packages, and the auxiliary
-libraries some of them use.
-
 Please read the following sections carefully.  If you are not
 comfortable with makefiles, or building codes on a Unix platform, or
 running an MPI job on your machine, please find a local expert to help
-you.  Many compilation, linking, and run problems that users have are
-often not really LAMMPS issues - they are peculiar to the user's
-system, compilers, libraries, etc.  Such questions are better answered
-by a local expert.
+you.  Many compilation, linking, and run problems users experience are
+often not LAMMPS issues - they are peculiar to the user's system,
+compilers, libraries, etc.  Such questions are better answered by a
+local expert.
 
 If you have a build problem that you are convinced is a LAMMPS issue
 (e.g. the compiler complains about a line of LAMMPS source code), then
@@ -413,7 +414,7 @@ uses (for performing 1d FFTs) when running the particle-particle
 particle-mesh (PPPM) option for long-range Coulombics via the
 "kspace_style"_kspace_style.html command.
 
-LAMMPS supports various open-source or vendor-supplied FFT libraries
+LAMMPS supports common open-source or vendor-supplied FFT libraries
 for this purpose.  If you leave these 3 variables blank, LAMMPS will
 use the open-source "KISS FFT library"_http://kissfft.sf.net, which is
 included in the LAMMPS distribution.  This library is portable to all
@@ -423,10 +424,9 @@ package in your build, you can also leave the 3 variables blank.
 
 Otherwise, select which kinds of FFTs to use as part of the FFT_INC
 setting by a switch of the form -DFFT_XXX.  Recommended values for XXX
-are: MKL, SCSL, FFTW2, and FFTW3.  Legacy options are: INTEL, SGI,
-ACML, and T3E.  For backward compatability, using -DFFT_FFTW will use
-the FFTW2 library.  Using -DFFT_NONE will use the KISS library
-described above.
+are: MKL or FFTW3.  FFTW2 and NONE are supported as legacy options.
+Selecting -DFFT_FFTW will use the FFTW3 library and -DFFT_NONE will
+use the KISS library described above.
 
 You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
 so the compiler and linker can find the needed FFT header and library
@@ -509,13 +509,13 @@ You should get the executable lmp_foo when the build is complete.
 
 Errors that can occur when making LAMMPS: h5 :link(start_2_3)
 
-NOTE: If an error occurs when building LAMMPS, the compiler or linker
-will state very explicitly what the problem is.  The error message
-should give you a hint as to which of the steps above has failed, and
-what you need to do in order to fix it.  Building a code with a
-Makefile is a very logical process.  The compiler and linker need to
-find the appropriate files and those files need to be compatible with
-LAMMPS source files.  When a make fails, there is usually a very
+If an error occurs when building LAMMPS, the compiler or linker will
+state very explicitly what the problem is.  The error message should
+give you a hint as to which of the steps above has failed, and what
+you need to do in order to fix it.  Building a code with a Makefile is
+a very logical process.  The compiler and linker need to find the
+appropriate files and those files need to be compatible with LAMMPS
+settings and source files.  When a make fails, there is usually a very
 simple reason, which you or a local expert will need to fix.
 
 Here are two non-obvious errors that can occur:
@@ -558,7 +558,8 @@ Typing "make clean-all" or "make clean-machine" will delete *.o object
 files created when LAMMPS is built, for either all builds or for a
 particular machine.
 
-Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
+Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
+-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
 
 As explained above, any of these 3 settings can be specified on the
 LMP_INC line in your low-level src/MAKE/Makefile.foo.
@@ -657,11 +658,6 @@ This section has the following sub-sections:
 2.3.3 "Packages that require extra libraries"_#start_3_3
 2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)
 
-Note that the following "Section 2.4"_#start_4 describes the Make.py
-tool which can be used to install/un-install packages and build the
-auxiliary libraries which some of them use.  It can also auto-edit a
-Makefile.machine to add settings needed by some packages.
-
 :line
 
 Package basics: :h5,link(start_3_1)
@@ -671,235 +667,221 @@ are always included, plus optional packages.  Packages are groups of
 files that enable a specific set of features.  For example, force
 fields for molecular systems or granular systems are in packages.
 
-"Section 4"_Section_packages.html in the manual has details
-about all the packages, including specific instructions for building
-LAMMPS with each package, which are covered in a more general manner
+"Section 4"_Section_packages.html in the manual has details about all
+the packages, which come in two flavors: [standard] and [user]
+packages. It also has specific instructions for building LAMMPS with
+any package which requires an extra library.  General instructions are
 below.
 
 You can see the list of all packages by typing "make package" from
-within the src directory of the LAMMPS distribution.  This also lists
-various make commands that can be used to manipulate packages.
+within the src directory of the LAMMPS distribution.  It will also
+list various make commands that can be used to manage packages.
 
 If you use a command in a LAMMPS input script that is part of a
 package, you must have built LAMMPS with that package, else you will
 get an error that the style is invalid or the command is unknown.
 Every command's doc page specfies if it is part of a package.  You can
-also type
+type
 
 lmp_machine -h :pre
 
 to run your executable with the optional "-h command-line
-switch"_#start_7 for "help", which will simply list the styles and
-commands known to your executable, and immediately exit.
-
-There are two kinds of packages in LAMMPS, standard and user packages.
-More information about the contents of standard and user packages is
-given in "Section 4"_Section_packages.html of the manual.  The
-difference between standard and user packages is as follows:
-
-Standard packages, such as molecule or kspace, are supported by the
-LAMMPS developers and are written in a syntax and style consistent
-with the rest of LAMMPS.  This means we will answer questions about
-them, debug and fix them if necessary, and keep them compatible with
-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 set of files grouped together which add a
-specific functionality to the code.
-
-User packages don't necessarily meet the requirements of the standard
-packages.  If you have problems using a feature provided in a user
-package, you may need to contact the contributor directly to get help.
-Information on how to submit additions you make to LAMMPS as single
-files or either a standard or user-contributed package are given in
-"this section"_Section_modify.html#mod_15 of the documentation.
+switch"_#start_7 for "help", which will list the styles and commands
+known to your executable, and immediately exit.
 
 :line
 
 Including/excluding packages :h5,link(start_3_2)
 
-To use (or not use) a package you must include it (or exclude it)
-before building LAMMPS.  From the src directory, this is typically as
-simple as:
+To use (or not use) a package you must install it (or un-install it)
+before building LAMMPS.  From the src directory, this is as simple as:
 
 make yes-colloid
 make mpi :pre
 
 or
 
-make no-manybody
+make no-user-omp
 make mpi :pre
 
-NOTE: You should NOT include/exclude packages and build LAMMPS in a
+NOTE: You should NOT install/un-install packages and build LAMMPS in a
 single make command using multiple targets, e.g. make yes-colloid mpi.
 This is because the make procedure creates a list of source files that
 will be out-of-date for the build if the package configuration changes
 within the same command.
 
-Some packages have individual files that depend on other packages
-being included.  LAMMPS checks for this and does the right thing.
-I.e. individual files are only included if their dependencies are
-already included.  Likewise, if a package is excluded, other files
+Any package can be installed or not in a LAMMPS build, independent of
+all other packages.  However, some packages include files derived from
+files in other packages.  LAMMPS checks for this and does the right
+thing.  I.e. individual files are only included if their dependencies
+are already included.  Likewise, if a package is excluded, other files
 dependent on that package are also excluded.
 
+NOTE: The one exception is that we do not recommend building with both
+the KOKKOS package installed and any of the other acceleration
+packages (GPU, OPT, USER-INTEL, USER-OMP) also installed.  This is
+because of how Kokkos sometimes builds using a wrapper compiler which
+can make it difficult to invoke all the compile/link flags correctly
+for both Kokkos and non-Kokkos files.
+
 If you will never run simulations that use the features in a
 particular packages, there is no reason to include it in your build.
-For some packages, this will keep you from having to build auxiliary
-libraries (see below), and will also produce a smaller executable
-which may run a bit faster.
+For some packages, this will keep you from having to build extra
+libraries, and will also produce a smaller executable which may run a
+bit faster.
 
-When you download a LAMMPS tarball, these packages are pre-installed
-in the src directory: KSPACE, MANYBODY,MOLECULE, because they are so
-commonly used.  When you download LAMMPS source files from the SVN or
-Git repositories, no packages are pre-installed.
+When you download a LAMMPS tarball, three packages are pre-installed
+in the src directory -- KSPACE, MANYBODY, MOLECULE -- because they are
+so commonly used.  When you download LAMMPS source files from the SVN
+or Git repositories, no packages are pre-installed.
 
-Packages are included or excluded by typing "make yes-name" or "make
-no-name", where "name" is the name of the package in lower-case, e.g.
-name = kspace for the KSPACE package or name = user-atc for the
-USER-ATC package.  You can also type "make yes-standard", "make
-no-standard", "make yes-std", "make no-std", "make yes-user", "make
-no-user", "make yes-lib", "make no-lib", "make yes-all", or "make
-no-all" to include/exclude various sets of packages.  Type "make
-package" to see all of the package-related make options.
+Packages are installed or un-installed by typing
 
-NOTE: Inclusion/exclusion of a package works by simply moving files
-back and forth between the main src directory and sub-directories with
-the package name (e.g. src/KSPACE, src/USER-ATC), so that the files
-are seen or not seen when LAMMPS is built.  After you have included or
-excluded a package, you must re-build LAMMPS.
+make yes-name
+make no-name :pre
 
-Additional package-related make options exist to help manage LAMMPS
-files that exist in both the src directory and in package
-sub-directories.  You do not normally need to use these commands
-unless you are editing LAMMPS files or have downloaded a patch from
-the LAMMPS WWW site.
+where "name" is the name of the package in lower-case, e.g.  name =
+kspace for the KSPACE package or name = user-atc for the USER-ATC
+package.  You can also type any of these commands:
 
-Typing "make package-update" or "make pu" will overwrite src files
-with files from the package sub-directories if the package has been
-included.  It should be used after a patch is installed, since patches
-only update the files in the package sub-directory, but not the src
-files.  Typing "make package-overwrite" will overwrite files in the
-package sub-directories with src files.
+make yes-all | install all packages
+make no-all | un-install all packages
+make yes-standard or make yes-std | install standard packages
+make no-standard or make no-std| un-install standard packages
+make yes-user | install user packages
+make no-user | un-install user packages
+make yes-lib | install packages that require extra libraries
+make no-lib | un-install packages that require extra libraries
+make yes-ext | install packages that require external libraries
+make no-ext | un-install packages that require external libraries :tb(s=|)
+
+which install/un-install various sets of packages.  Typing "make
+package" will list all the these commands.
+
+NOTE: Installing or un-installing a package works by simply moving
+files back and forth between the main src directory and
+sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
+so that the files are included or excluded when LAMMPS is built.
+After you have installed or un-installed a package, you must re-build
+LAMMPS for the action to take effect.
+
+The following make commands help manage files that exist in both the
+src directory and in package sub-directories.  You do not normally
+need to use these commands unless you are editing LAMMPS files or have
+downloaded a patch from the LAMMPS web site.
 
 Typing "make package-status" or "make ps" will show which packages are
-currently included. For those that are included, it will list any
+currently installed. For those that are installed, it will list any
 files that are different in the src directory and package
-sub-directory.  Typing "make package-diff" lists all differences
-between these files.  Again, type "make package" to see all of the
-package-related make options.
+sub-directory.
+
+Typing "make package-update" or "make pu" will overwrite src files
+with files from the package sub-directories if the package is
+installed.  It should be used after a patch has been applied, since
+patches only update the files in the package sub-directory, but not
+the src files.
+
+Typing "make package-overwrite" will overwrite files in the package
+sub-directories with src files.
+
+Typing "make package-diff" lists all differences between these files.
+
+Again, just type "make package" to see all of the package-related make
+options.
 
 :line
 
 Packages that require extra libraries :h5,link(start_3_3)
 
-A few of the standard and user packages require additional auxiliary
-libraries.  Many of them are provided with LAMMPS, in which case they
-must be compiled first, before LAMMPS is built, if you wish to include
-that package.  If you get a LAMMPS build error about a missing
-library, this is likely the reason.  See the
-"Section 4"_Section_packages.html doc page for a list of
-packages that have these kinds of auxiliary libraries.
+A few of the standard and user packages require extra libraries.  See
+"Section 4"_Section_packages.html for two tables of packages which
+indicate which ones require libraries.  For each such package, the
+Section 4 doc page gives details on how to build the extra library,
+including how to download it if necessary.  The basic ideas are
+summarized here.
 
-The lib directory in the distribution has sub-directories with package
-names that correspond to the needed auxiliary libs, e.g. lib/gpu.
-Each sub-directory has a README file that gives more details.  Code
-for most of the auxiliary libraries is included in that directory.
-Examples are the USER-ATC and MEAM packages.
+[System libraries:]
 
-A few of the lib sub-directories do not include code, but do include
-instructions (and sometimes scripts) that automate the process of
-downloading the auxiliary library and installing it so LAMMPS can link
-to it.  Examples are the KIM, VORONOI, USER-MOLFILE, and USER-SMD
-packages.
+Packages in the tables "Section 4"_Section_packages.html with a "sys"
+in the last column link to system libraries that typically already
+exist on your machine.  E.g. the python package links to a system
+Python library.  If your machine does not have the required library,
+you will have to download and install it on your machine, in either
+the system or user space.
 
-The lib/python directory (for the PYTHON package) contains only a
-choice of Makefile.lammps.* files.  This is because no auxiliary code
-or libraries are needed, only the Python library and other system libs
-that should already available on your system.  However, the
-Makefile.lammps file is needed to tell LAMMPS which libs to use and
-where to find them.
+[Internal libraries:]
 
-For libraries with provided code, the sub-directory README file
-(e.g. lib/atc/README) has instructions on how to build that library.
-This information is also summarized in "Section
-4"_Section_packages.html.  Typically this is done by typing
-something like:
+Packages in the tables "Section 4"_Section_packages.html with an "int"
+in the last column link to internal libraries whose source code is
+included with LAMMPS, in the lib/name directory where name is the
+package name.  You must first build the library in that directory
+before building LAMMPS with that package installed.  E.g. the gpu
+package links to a library you build in the lib/gpu dir.  You can
+often do the build in one step by typing "make lib-name args=..."
+from the src dir, with appropriate arguments.  You can leave off the
+args to see a help message.  See "Section 4"_Section_packages.html for
+details for each package.
 
-make -f Makefile.g++ :pre
+[External libraries:]
 
-If one of the provided Makefiles is not appropriate for your system
-you will need to edit or add one.  Note that all the Makefiles have a
-setting for EXTRAMAKE at the top that specifies a Makefile.lammps.*
-file.
+Packages in the tables "Section 4"_Section_packages.html with an "ext"
+in the last column link to exernal libraries whose source code is not
+included with LAMMPS.  You must first download and install the library
+before building LAMMPS with that package installed.  E.g. the voronoi
+package links to the freely available "Voro++ library"_voronoi.  You
+can often do the download/build in one step by typing "make lib-name
+args=..." from the src dir, with appropriate arguments.  You can leave
+off the args to see a help message.  See "Section
+4"_Section_packages.html for details for each package.
 
-If the library build is successful, it will produce 2 files in the lib
-directory:
+:link(voronoi,http://math.lbl.gov/voro++)
 
-libpackage.a
-Makefile.lammps :pre
+[Possible errors:]
 
-The Makefile.lammps file will typically be a copy of one of the
-Makefile.lammps.* files in the library directory.
+There are various common errors which can occur when building extra
+libraries or when building LAMMPS with packages that require the extra
+libraries.
 
-Note that you must insure that the settings in Makefile.lammps are
-appropriate for your system.  If they are not, the LAMMPS build may
-fail.  To fix this, you can edit or create a new Makefile.lammps.*
-file for your system, and copy it to Makefile.lammps.
+If you cannot build the extra library itself successfully, you may
+need to edit or create an appropriate Makefile for your machine, e.g.
+with appropriate compiler or system settings.  Provided makefiles are
+typically in the lib/name directory.  E.g. see the Makefile.* files in
+lib/gpu.
 
-As explained in the lib/package/README files, the settings in
-Makefile.lammps are used to specify additional system libraries and
-their locations so that LAMMPS can build with the auxiliary library.
-For example, if the MEAM package is used, the auxiliary library
-consists of F90 code, built with a Fortran complier.  To link that
-library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS is
-built with, typically requires additional Fortran-to-C libraries be
-included in the link.  Another example are the BLAS and LAPACK
-libraries needed to use the USER-ATC or USER-AWPMD packages.
+The LAMMPS build often uses settings in a lib/name/Makefile.lammps
+file which either exists in the LAMMPS distribution or is created or
+copied from a lib/name/Makefile.lammps.* file when the library is
+built.  If those settings are not correct for your machine you will
+need to edit or create an appropriate Makefile.lammps file.
 
-For libraries without provided code, the sub-directory README file has
-information on where to download the library and how to build it,
-e.g. lib/voronoi/README and lib/smd/README.  The README files also
-describe how you must either (a) create soft links, via the "ln"
-command, in those directories to point to where you built or installed
-the packages, or (b) check or edit the Makefile.lammps file in the
-same directory to provide that information.
+Package-specific details for these steps are given in "Section
+4"_Section_packages.html an in README files in the lib/name
+directories.
 
-Some of the sub-directories, e.g. lib/voronoi, also have an install.py
-script which can be used to automate the process of
-downloading/building/installing the auxiliary library, and setting the
-needed soft links.  Type "python install.py" for further instructions.
+[Compiler options needed for accelerator packages:]
 
-As with the sub-directories containing library code, if the soft links
-or settings in the lib/package/Makefile.lammps files are not correct,
-the LAMMPS build will typically fail.
+Several packages contain code that is optimized for specific hardware,
+e.g. CPU, KNL, or GPU.  These are the OPT, GPU, KOKKOS, USER-INTEL,
+and USER-OMP packages.  Compiling and linking the source files in
+these accelerator packages for optimal performance requires specific
+settings in the Makefile.machine file you use.
 
-:line
-
-Packages that require Makefile.machine settings :h5,link(start_3_4)
-
-A few packages require specific settings in Makefile.machine, to
-either build or use the package effectively.  These are the
-USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
-code performance on CPUs or other hardware, as discussed in "Section
-5.3"_Section_accelerate.html#acc_3.
-
-A summary of what Makefile.machine changes are needed for each of
-these packages is given in "Section 4"_Section_packages.html.
-The details are given on the doc pages that describe each of these
-accelerator packages in detail:
+A summary of the Makefile.machine settings needed for each of these
+packages is given in "Section 4"_Section_packages.html.  More info is
+given on the doc pages that describe each package in detail:
 
 5.3.1 "USER-INTEL package"_accelerate_intel.html
+5.3.2 "GPU package"_accelerate_intel.html
 5.3.3 "KOKKOS package"_accelerate_kokkos.html
 5.3.4 "USER-OMP package"_accelerate_omp.html
 5.3.5 "OPT package"_accelerate_opt.html :all(b)
 
-You can also look at the following machine Makefiles in
-src/MAKE/OPTIONS, which include the changes.  Note that the USER-INTEL
-and KOKKOS packages allow for settings that build LAMMPS for different
-hardware.  The USER-INTEL package builds for CPU and the Xeon Phi, the
-KOKKOS package builds for OpenMP, GPUs (Cuda), and the Xeon Phi.
+You can also use or examine the following machine Makefiles in
+src/MAKE/OPTIONS, which include the settings.  Note that the
+USER-INTEL and KOKKOS packages can use settings that build LAMMPS for
+different hardware.  The USER-INTEL package can be compiled for Intel
+CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs
+(Cuda), and Intel KNLs.
 
 Makefile.intel_cpu
 Makefile.intel_phi
@@ -909,127 +891,9 @@ Makefile.kokkos_phi
 Makefile.omp
 Makefile.opt :ul
 
-Also note that the Make.py tool, described in the next "Section
-2.4"_#start_4 can automatically add the needed info to an existing
-machine Makefile, using simple command-line arguments.
-
 :line
 
-2.4 Building LAMMPS via the Make.py tool :h4,link(start_4)
-
-The src directory includes a Make.py script, written in Python, which
-can be used to automate various steps of the build process.  It is
-particularly useful for working with the accelerator packages, as well
-as other packages which require auxiliary libraries to be built.
-
-The goal of the Make.py tool is to allow any complex multi-step LAMMPS
-build to be performed as a single Make.py command.  And you can
-archive the commands, so they can be re-invoked later via the -r
-(redo) switch.  If you find some LAMMPS build procedure that can't be
-done in a single Make.py command, let the developers know, and we'll
-see if we can augment the tool.
-
-You can run Make.py from the src directory by typing either:
-
-Make.py -h
-python Make.py -h :pre
-
-which will give you help info about the tool.  For the former to work,
-you may need to edit the first line of Make.py to point to your local
-Python.  And you may need to insure the script is executable:
-
-chmod +x Make.py :pre
-
-Here are examples of build tasks you can perform with Make.py:
-
-Install/uninstall packages: Make.py -p no-lib kokkos omp intel
-Build specific auxiliary libs: Make.py -a lib-atc lib-meam
-Build libs for all installed packages: Make.py -p cuda gpu -gpu mode=double arch=31 -a lib-all
-Create a Makefile from scratch with compiler and MPI settings: Make.py -m none -cc g++ -mpi mpich -a file
-Augment Makefile.serial with settings for installed packages: Make.py -p intel -intel cpu -m serial -a file
-Add JPG and FFTW support to Makefile.mpi: Make.py -m mpi -jpg -fft fftw -a file
-Build LAMMPS with a parallel make using Makefile.mpi: Make.py -j 16 -m mpi -a exe
-Build LAMMPS and libs it needs using Makefile.serial with accelerator settings: Make.py -p gpu intel -intel cpu -a lib-all file serial :tb(s=:)
-
-The bench and examples directories give Make.py commands that can be
-used to build LAMMPS with the various packages and options needed to
-run all the benchmark and example input scripts.  See these files for
-more details:
-
-bench/README
-bench/FERMI/README
-bench/KEPLER/README
-bench/PHI/README
-examples/README
-examples/accelerate/README
-examples/accelerate/make.list :ul
-
-All of the Make.py options and syntax help can be accessed by using
-the "-h" switch.
-
-E.g. typing "Make.py -h" gives
-
-Syntax: Make.py switch args ...
-  switches can be listed in any order
-  help switch:
-    -h prints help and syntax for all other specified switches
-  switch for actions:
-    -a lib-all, lib-dir, clean, file, exe or machine
-    list one or more actions, in any order
-    machine is a Makefile.machine suffix, must be last if used
-  one-letter switches:
-    -d (dir), -j (jmake), -m (makefile), -o (output),
-    -p (packages), -r (redo), -s (settings), -v (verbose)
-  switches for libs:
-    -atc, -awpmd, -colvars, -cuda
-    -gpu, -meam, -poems, -qmmm, -reax
-  switches for build and makefile options:
-    -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png :pre
-
-Using the "-h" switch with other switches and actions gives additional
-info on all the other specified switches or actions.  The "-h" can be
-anywhere in the command-line and the other switches do not need their
-arguments.  E.g. type "Make.py -h -d -atc -intel" will print:
-
--d dir
-  dir = LAMMPS home dir
-  if -d not specified, working dir must be lammps/src :pre
-
--atc make=suffix lammps=suffix2
-  all args are optional and can be in any order
-  make = use Makefile.suffix (def = g++)
-  lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile) :pre
-
--intel mode
-  mode = cpu or phi (def = cpu)
-    build Intel package for CPU or Xeon Phi :pre
-
-Note that Make.py never overwrites an existing Makefile.machine.
-Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
-rename if desired.  Likewise it creates an executable named
-src/lmp_auto, which you can rename using the -o switch if desired.
-
-The most recently executed Make.py commmand is saved in
-src/Make.py.last.  You can use the "-r" switch (for redo) to re-invoke
-the last command, or you can save a sequence of one or more Make.py
-commands to a file and invoke the file of commands using "-r".  You
-can also label the commands in the file and invoke one or more of them
-by name.
-
-A typical use of Make.py is to start with a valid Makefile.machine for
-your system, that works for a vanilla LAMMPS build, i.e. when optional
-packages are not installed.  You can then use Make.py to add various
-settings (FFT, JPG, PNG) to the Makefile.machine as well as change its
-compiler and MPI options.  You can also add additional packages to the
-build, as well as build the needed supporting libraries.
-
-You can also use Make.py to create a new Makefile.machine from
-scratch, using the "-m none" switch, if you also specify what compiler
-and MPI options to use, via the "-cc" and "-mpi" switches.
-
-:line
-
-2.5 Building LAMMPS as a library :h4,link(start_5)
+2.4 Building LAMMPS as a library :h4,link(start_4)
 
 LAMMPS can be built as either a static or shared library, which can
 then be called from another application or a scripting language.  See
@@ -1151,7 +1015,7 @@ interface and how to extend it for your needs.
 
 :line
 
-2.6 Running LAMMPS :h4,link(start_6)
+2.5 Running LAMMPS :h4,link(start_5)
 
 By default, LAMMPS runs by reading commands from standard input.  Thus
 if you run the LAMMPS executable by itself, e.g.
@@ -1283,7 +1147,7 @@ more processors or setup a smaller problem.
 
 :line
 
-2.7 Command-line options :h4,link(start_7)
+2.6 Command-line options :h4,link(start_6)
 
 At run time, LAMMPS recognizes several optional command-line switches
 which may be used in any order.  Either the full word or a one-or-two
@@ -1713,7 +1577,7 @@ negative numeric value.  It is OK if the first value1 starts with a
 
 :line
 
-2.8 LAMMPS screen output :h4,link(start_8)
+2.7 LAMMPS screen output :h4,link(start_7)
 
 As LAMMPS reads an input script, it prints information to both the
 screen and a log file about significant actions it takes to setup a
@@ -1869,7 +1733,7 @@ communication, roughly 75% in the example above.
 
 :line
 
-2.9 Tips for users of previous LAMMPS versions :h4,link(start_9)
+2.8 Tips for users of previous LAMMPS versions :h4,link(start_8)
 
 The current C++ began with a complete rewrite of LAMMPS 2001, which
 was written in F90.  Features of earlier versions of LAMMPS are listed

doc/src/Section_tools.txt

@@ -12,9 +12,12 @@ Section"_Section_modify.html :c
 
 LAMMPS is designed to be a computational kernel for performing
 molecular dynamics computations.  Additional pre- and post-processing
-steps are often necessary to setup and analyze a simulation.  A few
-additional tools are provided with the LAMMPS distribution and are
-described in this section.
+steps are often necessary to setup and analyze a simulation. A
+list of such tools can be found on the LAMMPS home page
+at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html
+
+A few additional tools are provided with the LAMMPS distribution
+and are described in this section.
 
 Our group has also written and released a separate toolkit called
 "Pizza.py"_pizza which provides tools for doing setup, analysis,
@@ -36,16 +39,16 @@ authors.
 The source code for each of these codes is in the tools sub-directory
 of the LAMMPS distribution.  There is a Makefile (which you may need
 to edit for your platform) which will build several of the tools which
-reside in that directory.  Some of them are larger packages in their
-own sub-directories with their own Makefiles.
+reside in that directory.  Most of them are larger packages in their
+own sub-directories with their own Makefiles and/or README files.
 
 "amber2lmp"_#amber
 "binary2txt"_#binary
 "ch2lmp"_#charmm
 "chain"_#chain
 "colvars"_#colvars
-"createatoms"_#create
-"data2xmovie"_#data
+"createatoms"_#createatoms
+"drude"_#drude
 "eam database"_#eamdb
 "eam generate"_#eamgn
 "eff"_#eff
@@ -56,20 +59,18 @@ own sub-directories with their own Makefiles.
 "kate"_#kate
 "lmp2arc"_#arc
 "lmp2cfg"_#cfg
-"lmp2vmd"_#vmd
 "matlab"_#matlab
 "micelle2d"_#micelle
 "moltemplate"_#moltemplate
 "msi2lmp"_#msi
 "phonon"_#phonon
-"polymer bonding"_#polybond
+"polybond"_#polybond
 "pymol_asphere"_#pymol
 "python"_#pythontools
 "reax"_#reax_tool
-"restart2data"_#restart
+"smd"_#smd
 "vim"_#vim
 "xmgrace"_#xmgrace
-"xmovie"_#xmovie :ul
 
 :line
 
@@ -158,7 +159,7 @@ gmail.com) at ICTP, Italy.
 
 :line
 
-createatoms tool :h4,link(create)
+createatoms tool :h4,link(createatoms)
 
 The tools/createatoms directory contains a Fortran program called
 createAtoms.f which can generate a variety of interesting crystal
@@ -171,16 +172,16 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
 
 :line
 
-data2xmovie tool :h4,link(data)
+drude tool :h4,link(drude)
 
-The file data2xmovie.c converts a LAMMPS data file into a snapshot
-suitable for visualizing with the "xmovie"_#xmovie tool, as if it had
-been output with a dump command from LAMMPS itself.  The syntax for
-running the tool is
+The tools/drude directory contains a Python script called
+polarizer.py which can add Drude oscillators to a LAMMPS
+data file in the required format.
 
-data2xmovie \[options\] < infile > outfile :pre
+See the header of the polarizer.py file for details.
 
-See the top of the data2xmovie.c file for a discussion of the options.
+The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua
+at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
 
 :line
 
@@ -317,18 +318,6 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
 
 :line
 
-lmp2vmd tool :h4,link(vmd)
-
-The lmp2vmd sub-directory contains a README.txt file that describes
-details of scripts and plugin support within the "VMD
-package"_http://www.ks.uiuc.edu/Research/vmd for visualizing LAMMPS
-dump files.
-
-The VMD plugins and other supporting scripts were written by Axel
-Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
-
-:line
-
 matlab tool :h4,link(matlab)
 
 The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
@@ -380,17 +369,18 @@ supports it.  It has its own WWW page at
 
 msi2lmp tool :h4,link(msi)
 
-The msi2lmp sub-directory contains a tool for creating LAMMPS input
-data files from Accelrys' Insight MD code (formerly MSI/Biosym and
-its Discover MD code).  See the README file for more information.
+The msi2lmp sub-directory contains a tool for creating LAMMPS template
+input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
+Insight MD code, formerly MSI/Biosym and its Discover MD code).
 
 This tool was written by John Carpenter (Cray), Michael Peachey
-(Cray), and Steve Lustig (Dupont).  John is now at the Mayo Clinic
-(jec at mayo.edu), but still fields questions about the tool.
+(Cray), and Steve Lustig (Dupont). Several people contributed changes
+to remove bugs and adapt its output to changes in LAMMPS.
 
-This tool may be out-of-date with respect to the current LAMMPS and
-Insight versions.  Since we don't use it at Sandia, you'll need to
-experiment with it yourself.
+This tool has several known limitations and is no longer under active
+development, so there are no changes except for the occasional bugfix.
+
+See the README file in the tools/msi2lmp folder for more information.
 
 :line
 
@@ -409,7 +399,7 @@ University.
 
 :line
 
-polymer bonding tool :h4,link(polybond)
+polybond tool :h4,link(polybond)
 
 The polybond sub-directory contains a Python-based tool useful for
 performing "programmable polymer bonding".  The Python file
@@ -468,48 +458,19 @@ These tools were written by Aidan Thompson at Sandia.
 
 :line
 
-restart2data tool :h4,link(restart)
+smd tool :h4,link(smd)
 
-NOTE: This tool is now obsolete and is not included in the current
-LAMMPS distribution.  This is becaues there is now a
-"write_data"_write_data.html command, which can create a data file
-from within an input script.  Running LAMMPS with the "-r"
-"command-line switch"_Section_start.html#start_7 as follows:
+The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
+Makefile which can be compiled and used to convert triangle output
+files created by the Smooth-Mach Dynamics (USER-SMD) package into a
+VTK-compatible unstructured grid file.  It could then be read in and
+visualized by VTK.
 
-lmp_g++ -r restartfile datafile
+See the header of dump2vtk.cpp for more details.
 
-is the same as running a 2-line input script:
-
-read_restart restartfile
-write_data datafile
-
-which will produce the same data file that the restart2data tool used
-to create.  The following information is included in case you have an
-older version of LAMMPS which still includes the restart2data tool.
-
-The file restart2data.cpp converts a binary LAMMPS restart file into
-an ASCII data file.  The syntax for running the tool is
-
-restart2data restart-file data-file (input-file) :pre
-
-Input-file is optional and if specified will contain LAMMPS input
-commands for the masses and force field parameters, instead of putting
-those in the data-file.  Only a few force field styles currently
-support this option.
-
-This tool must be compiled on a platform that can read the binary file
-created by a LAMMPS run, since binary files are not compatible across
-all platforms.
-
-Note that a text data file has less precision than a binary restart
-file.  Hence, continuing a run from a converted data file will
-typically not conform as closely to a previous run as will restarting
-from a binary restart file.
-
-If a "%" appears in the specified restart-file, the tool expects a set
-of multiple files to exist.  See the "restart"_restart.html and
-"write_restart"_write_restart.html commands for info on how such sets
-of files are written by LAMMPS, and how the files are named.
+This tool was written by the USER-SMD package author, Georg
+Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics,
+Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
 
 :line
 
@@ -537,32 +498,3 @@ See the README file for details.
 
 These files were provided by Vikas Varshney (vv0210 at gmail.com)
 
-:line
-
-xmovie tool :h4,link(xmovie)
-
-The xmovie tool is an X-based visualization package that can read
-LAMMPS dump files and animate them.  It is in its own sub-directory
-with the tools directory.  You may need to modify its Makefile so that
-it can find the appropriate X libraries to link against.
-
-The syntax for running xmovie is
-
-xmovie \[options\] dump.file1 dump.file2 ... :pre
-
-If you just type "xmovie" you will see a list of options.  Note that
-by default, LAMMPS dump files are in scaled coordinates, so you
-typically need to use the -scale option with xmovie.  When xmovie runs
-it opens a visualization window and a control window.  The control
-options are straightforward to use.
-
-Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he
-spent a summer at Sandia.  It displays 2d projections of a 3d domain.
-While simple in design, it is an amazingly fast program that can
-render large numbers of atoms very quickly.  It's a useful tool for
-debugging LAMMPS input and output and making sure your simulation is
-doing what you think it should.  The animations on the Examples page
-of the "LAMMPS WWW site"_lws were created with xmovie.
-
-I've lost contact with Mike, so I hope he's comfortable with us
-distributing his great tool!

doc/src/USER/atc/man_consistent_fe_initialization.html

@@ -27,7 +27,7 @@
 syntax</a></h2>
 <p>fix_modify AtC consistent_fe_initialization &lt;on | off&gt;</p>
 <ul>
-<li>&lt;on|off&gt; = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field </li>
+<li>&lt;on|off&gt; = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field </li>
 </ul>
 <h2><a class="anchor" id="examples">
 examples</a></h2>

doc/src/accelerate_intel.txt

@@ -20,7 +20,7 @@ coprocessors via offloading neighbor list and non-bonded force
 calculations to the Phi.  The same C++ code is used in both cases.
 When offloading to a coprocessor from a CPU, the same routine is run
 twice, once on the CPU and once with an offload flag. This allows
-LAMMPS to run on the CPU cores and coprocessor cores simulataneously.
+LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
 
 [Currently Available USER-INTEL Styles:]
 
@@ -115,7 +115,7 @@ coprocessor and an Intel compiler are required. For this, the
 recommended version of the Intel compiler is 14.0.1.106 or
 versions 15.0.2.044 and higher.
 
-Although any compiler can be used with the USER-INTEL pacakge,
+Although any compiler can be used with the USER-INTEL package,
 currently, vectorization directives are disabled by default when
 not using Intel compilers due to lack of standard support and
 observations of decreased performance. The OpenMP standard now
@@ -428,7 +428,7 @@ to the card.  This allows for overlap of MPI communication of forces
 with computation on the coprocessor when the "newton"_newton.html
 setting is "on".  The default is dependent on the style being used,
 however, better performance may be achieved by setting this option
-explictly.
+explicitly.
 
 When using offload with CPU Hyper-Threading disabled, it may help
 performance to use fewer MPI tasks and OpenMP threads than available
@@ -464,7 +464,7 @@ supported.
 
 [References:]
 
-Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., “Optimizing Classical Molecular Dynamics in LAMMPS,” in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
+Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
 
 Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l
 

doc/src/accelerate_kokkos.txt

@@ -217,7 +217,7 @@ best performance its CCFLAGS setting should use -O3 and have a
 KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
 hardware and software installation, e.g. KOKKOS_ARCH=Kepler30.  Note
 the minimal required compute capability is 2.0, but this will give
-signicantly reduced performance compared to Kepler generation GPUs
+significantly reduced performance compared to Kepler generation GPUs
 with compute capability 3.x.  For the LINK setting, "nvcc" should not
 be used; instead use g++ or another compiler suitable for linking C++
 applications.  Often you will want to use your MPI compiler wrapper
@@ -234,7 +234,7 @@ provides alternative methods via environment variables for binding
 threads to hardware cores.  More info on binding threads to cores is
 given in "Section 5.3"_Section_accelerate.html#acc_3.
 
-KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
+KOKKOS_ARCH=KNC enables compiler switches needed when compiling for an
 Intel Phi processor.
 
 KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
@@ -272,7 +272,7 @@ coprocessor support you need to insure there are one or more MPI tasks
 per coprocessor, and choose the number of coprocessor threads to use
 per MPI task (via the "-k" command-line switch discussed below).  The
 product of MPI tasks * coprocessor threads/task should not exceed the
-maximum number of threads the coproprocessor is designed to run,
+maximum number of threads the coprocessor is designed to run,
 otherwise performance will suffer.  This value is 240 for current
 generation Xeon Phi(TM) chips, which is 60 physical cores * 4
 threads/core.  Note that with the KOKKOS package you do not need to
@@ -333,7 +333,7 @@ device=CUDA are the same.
 
 You must still use the "-k on" "command-line
 switch"_Section_start.html#start_7 to enable the KOKKOS package, and
-specify its additional arguments for hardware options appopriate to
+specify its additional arguments for hardware options appropriate to
 your system, as documented above.
 
 Use the "suffix kk"_suffix.html command, or you can explicitly add a

doc/src/angle_class2.txt

@@ -8,6 +8,7 @@
 
 angle_style class2 command :h3
 angle_style class2/omp command :h3
+angle_style class2/kk command :h3
 
 [Syntax:]
 

doc/src/angle_dipole.txt

@@ -41,7 +41,7 @@ angle.
 
 The torque on the dipole can be obtained by differentiating the
 potential using the 'chain rule' as in appendix C.3 of
-"(Allen)"_#Allen:
+"(Allen)"_#Allen1:
 
 :c,image(Eqs/angle_dipole_torque.jpg)
 
@@ -121,6 +121,6 @@ This angle style should not be used with SHAKE.
 [(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of
 lipid membranes, PloS ONE 6(12): e28637, 2011.
 
-:link(Allen)
+:link(Allen1)
 [(Allen)] Allen & Tildesley, Computer Simulation of Liquids,
 Clarendon Press, Oxford, 1987.

doc/src/angle_hybrid.txt

@@ -81,7 +81,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 Unlike other angle styles, the hybrid angle style does not store angle
 coefficient info for individual sub-styles in a "binary restart
-files"_restart.html.  Thus when retarting a simulation from a restart
+files"_restart.html.  Thus when restarting a simulation from a restart
 file, you need to re-specify angle_coeff commands.
 
 [Related commands:]

doc/src/angle_sdk.txt

@@ -46,7 +46,7 @@ from the pair_style.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-USER-CG-CMM package.  See the "Making
+USER-CGSDK package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/atom_modify.txt

@@ -103,7 +103,7 @@ turns off the {first} option.
 
 It is OK to use the {first} keyword with a group that has not yet been
 defined, e.g. to use the atom_modify first command at the beginning of
-your input script.  LAMMPS does not use the group until a simullation
+your input script.  LAMMPS does not use the group until a simulation
 is run.
 
 The {sort} keyword turns on a spatial sorting or reordering of atoms
@@ -116,7 +116,7 @@ various other factors.  As a general rule, sorting is typically more
 effective at speeding up simulations of liquids as opposed to solids.
 In tests we have done, the speed-up can range from zero to 3-4x.
 
-Reordering is peformed every {Nfreq} timesteps during a dynamics run
+Reordering is performed every {Nfreq} timesteps during a dynamics run
 or iterations during a minimization.  More precisely, reordering
 occurs at the first reneighboring that occurs after the target
 timestep.  The reordering is performed locally by each processor,
@@ -130,7 +130,7 @@ the processor's 1d list of atoms.
 The goal of this procedure is for atoms to put atoms close to each
 other in the processor's one-dimensional list of atoms that are also
 near to each other spatially.  This can improve cache performance when
-pairwise intereractions and neighbor lists are computed.  Note that if
+pairwise interactions and neighbor lists are computed.  Note that if
 bins are too small, there will be few atoms/bin.  Likewise if bins are
 too large, there will be many atoms/bin.  In both cases, the goal of
 cache locality will be undermined.
@@ -138,7 +138,7 @@ cache locality will be undermined.
 NOTE: Running a simulation with sorting on versus off should not
 change the simulation results in a statistical sense.  However, a
 different ordering will induce round-off differences, which will lead
-to diverging trajectories over time when comparing two simluations.
+to diverging trajectories over time when comparing two simulations.
 Various commands, particularly those which use random numbers
 (e.g. "velocity create"_velocity.html, and "fix
 langevin"_fix_langevin.html), may generate (statistically identical)

doc/src/atom_style.txt

@@ -110,12 +110,17 @@ basis.
 For the {sphere} style, the particles are spheres and each stores a
 per-particle diameter and mass.  If the diameter > 0.0, the particle
 is a finite-size sphere.  If the diameter = 0.0, it is a point
-particle.
+particle.  Note that by use of the {disc} keyword with the "fix
+nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html,
+"fix nph/sphere"_fix_nph_sphere.html, "fix
+npt/sphere"_fix_npt_sphere.html commands, spheres can be effectively
+treated as 2d discs for a 2d simulation if desired.  See also the "set
+density/disc"_set.html command.
 
 For the {ellipsoid} style, the particles are ellipsoids and each
 stores a flag which indicates whether it is a finite-size ellipsoid or
 a point particle.  If it is an ellipsoid, it also stores a shape
-vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
+vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
 with its orientation.
 
 For the {dipole} style, a point dipole is defined for each point
@@ -149,7 +154,7 @@ Hydrodynamics.  Both fluids and solids can be modeled.  Particles
 store the mass and volume of an integration point, a kernel diameter
 used for calculating the field variables (e.g. stress and deformation)
 and a contact radius for calculating repulsive forces which prevent
-individual physical bodies from penetretating each other.
+individual physical bodies from penetrating each other.
 
 The {wavepacket} style is similar to {electron}, but the electrons may
 consist of several Gaussian wave packets, summed up with coefficients
@@ -165,7 +170,7 @@ For the {tri} style, the particles are planar triangles and each
 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
+The {template} style allows molecular topology (bonds,angles,etc) to be
 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
@@ -195,7 +200,7 @@ the {bstyle} argument.  Body particles can represent complex entities,
 such as surface meshes of discrete points, collections of
 sub-particles, deformable objects, etc.
 
-The "body"_body.html doc page descibes the body styles LAMMPS
+The "body"_body.html doc page describes the body styles LAMMPS
 currently supports, and provides more details as to the kind of body
 particles they represent.  For all styles, each body particle stores
 moments of inertia and a quaternion 4-vector, so that its orientation
@@ -280,7 +285,7 @@ The {dpd} style is part of the USER-DPD package for dissipative
 particle dynamics (DPD).
 
 The {meso} style is part of the USER-SPH package for smoothed particle
-hydrodyanmics (SPH).  See "this PDF
+hydrodynamics (SPH).  See "this PDF
 guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
 
 The {wavepacket} style is part of the USER-AWPMD package for the

doc/src/balance.txt

@@ -12,7 +12,7 @@ balance command :h3
 
 balance thresh style args ... keyword args ... :pre
 
-thresh = imbalance threshhold that must be exceeded to perform a re-balance :ulb,l
+thresh = imbalance threshold that must be exceeded to perform a re-balance :ulb,l
 one style/arg pair can be used (or multiple for {x},{y},{z}) :l
 style = {x} or {y} or {z} or {shift} or {rcb} :l
   {x} args = {uniform} or Px-1 numbers between 0 and 1
@@ -30,7 +30,7 @@ style = {x} or {y} or {z} or {shift} or {rcb} :l
   {shift} args = dimstr Niter stopthresh
     dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
     Niter = # of times to iterate within each dimension of dimstr sequence
-    stopthresh = stop balancing when this imbalance threshhold is reached
+    stopthresh = stop balancing when this imbalance threshold is reached
   {rcb} args = none :pre
 zero or more keyword/arg pairs may be appended :l
 keyword = {weight} or {out} :l
@@ -76,13 +76,13 @@ sub-domain sizes and shapes on-the-fly during a "run"_run.html.
 
 Load-balancing is typically most useful if the particles in the
 simulation box have a spatially-varying density distribution or when
-the computational cost varies signficantly between different
+the computational cost varies significantly between different
 particles.  E.g. a model of a vapor/liquid interface, or a solid with
 an irregular-shaped geometry containing void regions, or "hybrid pair
 style simulations"_pair_hybrid.html which combine pair styles with
 different computational cost.  In these cases, the LAMMPS default of
 dividing the simulation box volume into a regular-spaced grid of 3d
-bricks, with one equal-volume sub-domain per procesor, may assign
+bricks, with one equal-volume sub-domain per processor, may assign
 numbers of particles per processor in a way that the computational
 effort varies significantly.  This can lead to poor performance when
 the simulation is run in parallel.
@@ -91,7 +91,7 @@ The balancing can be performed with or without per-particle weighting.
 With no weighting, the balancing attempts to assign an equal number of
 particles to each processor.  With weighting, the balancing attempts
 to assign an equal aggregate computational weight to each processor,
-which typically inducces a diffrent number of atoms assigned to each
+which typically induces a different number of atoms assigned to each
 processor.  Details on the various weighting options and examples for
 how they can be used are "given below"_#weighted_balance.
 
@@ -222,7 +222,7 @@ listed in ascending order.  They represent the fractional position of
 the cutting place.  The left (or lower) edge of the box is 0.0, and
 the right (or upper) edge is 1.0.  Neither of these values is
 specified.  Only the interior Ps-1 positions are specified.  Thus is
-there are 2 procesors in the x dimension, you specify a single value
+there are 2 processors in the x dimension, you specify a single value
 such as 0.75, which would make the left processor's sub-domain 3x
 larger than the right processor's sub-domain.
 
@@ -266,7 +266,7 @@ assigned, particles are migrated to their new owning processor, and
 the balance procedure ends.
 
 NOTE: At each rebalance operation, the bisectioning for each cutting
-plane (line in 2d) typcially starts with low and high bounds separated
+plane (line in 2d) typically starts with low and high bounds separated
 by the extent of a processor's sub-domain in one dimension.  The size
 of this bracketing region shrinks by 1/2 every iteration.  Thus if
 {Niter} is specified as 10, the cutting plane will typically be
@@ -286,24 +286,32 @@ above.  It performs a recursive coordinate bisectioning (RCB) of the
 simulation domain. The basic idea is as follows.
 
 The simulation domain is cut into 2 boxes by an axis-aligned cut in
-the longest dimension, leaving one new box on either side of the cut.
-All the processors are also partitioned into 2 groups, half assigned
-to the box on the lower side of the cut, and half to the box on the
-upper side.  (If the processor count is odd, one side gets an extra
-processor.)  The cut is positioned so that the number of particles in
-the lower box is exactly the number that the processors assigned to
-that box should own for load balance to be perfect.  This also makes
-load balance for the upper box perfect.  The positioning is done
-iteratively, by a bisectioning method.  Note that counting particles
-on either side of the cut requires communication between all
-processors at each iteration.
+one of the dimensions, leaving one new sub-box on either side of the
+cut.  Which dimension is chosen for the cut depends on the particle
+(weight) distribution within the parent box.  Normally the longest
+dimension of the box is cut, but if all (or most) of the particles are
+at one end of the box, a cut may be performed in another dimension to
+induce sub-boxes that are more cube-ish (3d) or square-ish (2d) in
+shape.
+
+After the cut is made, all the processors are also partitioned into 2
+groups, half assigned to the box on the lower side of the cut, and
+half to the box on the upper side.  (If the processor count is odd,
+one side gets an extra processor.)  The cut is positioned so that the
+number of (weighted) particles in the lower box is exactly the number
+that the processors assigned to that box should own for load balance
+to be perfect.  This also makes load balance for the upper box
+perfect.  The positioning of the cut is done iteratively, by a
+bisectioning method (median search).  Note that counting particles on
+either side of the cut requires communication between all processors
+at each iteration.
 
 That is the procedure for the first cut.  Subsequent cuts are made
 recursively, in exactly the same manner.  The subset of processors
-assigned to each box make a new cut in the longest dimension of that
-box, splitting the box, the subset of processsors, and the particles
-in the box in two.  The recursion continues until every processor is
-assigned a sub-box of the entire simulation domain, and owns the
+assigned to each box make a new cut in one dimension of that box,
+splitting the box, the subset of processors, and the particles in the
+box in two.  The recursion continues until every processor is assigned
+a sub-box of the entire simulation domain, and owns the (weighted)
 particles in that sub-box.
 
 :line
@@ -368,7 +376,7 @@ of about 0.8 often results in the best performance, since the number
 of neighbors is likely to overestimate the ideal weight.
 
 This weight style is useful for systems where there are different
-cutoffs used for different pairs of interations, or the density
+cutoffs used for different pairs of interactions, or the density
 fluctuates, or a large number of particles are in the vicinity of a
 wall, or a combination of these effects.  If a simulation uses
 multiple neighbor lists, this weight style will use the first suitable
@@ -402,7 +410,7 @@ decrease the weights so that the ratio of max weight to min weight
 decreases by {factor}.  In both cases the intermediate weight values
 increase/decrease proportionally as well.  A value = 1.0 has no effect
 on the {time} weights.  As a rule of thumb, effective values to use
-are typicall between 0.5 and 1.2.  Note that the timer quantities
+are typically between 0.5 and 1.2.  Note that the timer quantities
 mentioned above can be affected by communication which occurs in the
 middle of the operations, e.g. pair styles with intermediate exchange
 of data witin the force computation, and likewise for KSpace solves.

doc/src/body.txt

@@ -82,7 +82,7 @@ internal stress that induces fragmentation :ul
 then the interaction between pairs of particles is likely to be more
 complex than the summation of simple sub-particle interactions.  An
 example is contact or frictional forces between particles with planar
-sufaces that inter-penetrate.
+surfaces that inter-penetrate.
 
 These are additional LAMMPS commands that can be used with body
 particles of different styles
@@ -105,7 +105,7 @@ in the sections below.
 
 The {nparticle} body style represents body particles as a rigid body
 with a variable number N of sub-particles.  It is provided as a
-vanillia, prototypical example of a body particle, although as
+vanilla, prototypical example of a body particle, although as
 mentioned above, the "fix rigid"_fix_rigid.html command already
 duplicates its functionality.
 
@@ -140,7 +140,7 @@ for more details.
 The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
 values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
-simulation box XYZ axes, not with respect to the prinicpal axes of the
+simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
 The coordinates of each sub-particle are specified as its x,y,z
 displacement from the center-of-mass of the body particle.  The
@@ -218,7 +218,7 @@ wish; see the "read_data"_read_data.html command for more details.
 The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
 values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
-simulation box XYZ axes, not with respect to the prinicpal axes of the
+simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
 The coordinates of each vertex are specified as its x,y,z displacement
 from the center-of-mass of the body particle.  The center-of-mass

doc/src/bond_class2.txt

@@ -8,6 +8,7 @@
 
 bond_style class2 command :h3
 bond_style class2/omp command :h3
+bond_style class2/kk command :h3
 
 [Syntax:]
 

doc/src/bond_hybrid.txt

@@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 Unlike other bond styles, the hybrid bond style does not store bond
 coefficient info for individual sub-styles in a "binary restart
-files"_restart.html.  Thus when retarting a simulation from a restart
+files"_restart.html.  Thus when restarting a simulation from a restart
 file, you need to re-specify bond_coeff commands.
 
 [Related commands:]

doc/src/bond_oxdna.txt

@@ -6,20 +6,25 @@
 
 :line
 
-bond_style oxdna_fene command :h3
+bond_style oxdna/fene command :h3
+bond_style oxdna2/fene command :h3
 
 [Syntax:]
 
-bond_style oxdna_fene :pre
+bond_style oxdna/fene :pre
+bond_style oxdna2/fene :pre
 
 [Examples:]
 
-bond_style oxdna_fene
+bond_style oxdna/fene
 bond_coeff * 2.0 0.25 0.7525 :pre
 
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564 :pre
+
 [Description:]
 
-The {oxdna_fene} bond style uses the potential
+The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
 
 :c,image(Eqs/bond_oxdna_fene.jpg)
 
@@ -36,15 +41,16 @@ epsilon (energy)
 Delta (distance)
 r0 (distance) :ul
 
-NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
-for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
-and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of 
-"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients 
-in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
+NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles
+for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
+and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of 
+"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair 
+style {oxdna2/dh} have to be defined.
+The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
 
-Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
+Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
 A simple python setup tool which creates single straight or helical DNA strands,
-DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
+DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
 A technical report with more information on the model, the structure of the input file,
 the setup tool and the performance of the LAMMPS-implementation of oxDNA
 can be found "here"_PDF/USER-CGDNA-overview.pdf.
@@ -60,7 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]
 
-"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
+"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
 
 [Default:] none
 
@@ -68,3 +74,6 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :link(oxdna_fene)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
+
+:link(oxdna2)
+[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).

doc/src/bonds.txt

@@ -15,7 +15,7 @@ Bond Styles :h1
    bond_morse
    bond_none
    bond_nonlinear
-   bond_oxdna_fene
+   bond_oxdna
    bond_quartic
    bond_table
    bond_zero

doc/src/change_box.txt

@@ -101,11 +101,11 @@ Instead you could do something like this, assuming the simulation box
 is non-periodic and atoms extend from 0 to 20 in all dimensions:
 
 change_box all x final -10 20
-create_atoms 1 single -5 5 5   # this will fail to insert an atom :pre
+create_atoms 1 single -5 5 5       # this will fail to insert an atom :pre
 
 change_box all x final -10 20 boundary f s s
 create_atoms 1 single -5 5 5
-change_box boundary s s s      # this will work :pre
+change_box all boundary s s s      # this will work :pre
 
 NOTE: Unlike the earlier "displace_box" version of this command, atom
 remapping is NOT performed by default.  This command allows remapping
@@ -258,8 +258,8 @@ command.
 :line
 
 The {ortho} and {triclinic} keywords convert the simulation box to be
-orthogonal or triclinic (non-orthongonal).  See "this
-section"_Section_howto#howto_13 for a discussion of how non-orthongal
+orthogonal or triclinic (non-orthogonal).  See "this
+section"_Section_howto#howto_13 for a discussion of how non-orthogonal
 boxes are represented in LAMMPS.
 
 The simulation box is defined as either orthogonal or triclinic when
@@ -289,7 +289,7 @@ the create_box command is encountered in the input script.
 The {remap} keyword remaps atom coordinates from the last saved box
 size/shape to the current box state.  For example, if you stretch the
 box in the x dimension or tilt it in the xy plane via the {x} and {xy}
-keywords, then the {remap} commmand will dilate or tilt the atoms to
+keywords, then the {remap} command will dilate or tilt the atoms to
 conform to the new box size/shape, as if the atoms moved with the box
 as it deformed.
 

doc/src/comm_style.txt

@@ -39,7 +39,7 @@ sizes and shapes.  Again there is one tile per processor.  To acquire
 information for nearby atoms, communication must now be done with a
 more complex pattern of neighboring processors.
 
-Note that this command does not actually define a partitoining of the
+Note that this command does not actually define a partitioning of the
 simulation box (a domain decomposition), rather it determines what
 kinds of decompositions are allowed and the pattern of communication
 used to enable the decomposition.  A decomposition is created when the

doc/src/compute.txt

@@ -235,7 +235,7 @@ section of "this page"_Section_commands.html#cmd_5.
 "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
 "temp/region"_compute_temp_region.html - temperature of a region of atoms
 "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
-"ti"_compute_ti.html - thermodyanmic integration free energy values
+"ti"_compute_ti.html - thermodynamic integration free energy values
 "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
 "vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms
 "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk

doc/src/compute_angmom_chunk.txt

@@ -22,7 +22,7 @@ compute 1 fluid angmom/chunk molchunk :pre
 
 [Description:]
 
-Define a computation that calculates the angular momemtum of multiple
+Define a computation that calculates the angular momentum of multiple
 chunks of atoms.
 
 In LAMMPS, chunks are collections of atoms defined by a "compute

doc/src/compute_centro_atom.txt

@@ -18,8 +18,8 @@ lattice = {fcc} or {bcc} or N = # of neighbors per atom to include :l
 zero or more keyword/value pairs may be appended :l
 keyword = {axes} :l
   {axes} value = {no} or {yes}
-    {no} = do not calulate 3 symmetry axes
-    {yes} = calulate 3 symmetry axes :pre
+    {no} = do not calculate 3 symmetry axes
+    {yes} = calculate 3 symmetry axes :pre
 :ule
 
 [Examples:]
@@ -108,7 +108,7 @@ symmetry axis, followed by the second, and third symmetry axes in
 columns 5-7 and 8-10.
 
 The centrosymmetry values are unitless values >= 0.0.  Their magnitude
-depends on the lattice style due to the number of contibuting neighbor
+depends on the lattice style due to the number of contributing neighbor
 pairs in the summation in the formula above.  And it depends on the
 local defects surrounding the central atom, as described above.  For
 the {axes yes} case, the vector components are also unitless, since

doc/src/compute_chunk_atom.txt

@@ -148,7 +148,9 @@ described further below where the keywords are discussed.
 The {binning} styles perform a spatial binning of atoms, and assign an
 atom the chunk ID corresponding to the bin number it is in.  {Nchunk}
 is set to the number of bins, which can change if the simulation box
-size changes.
+size changes.  This also depends on the setting of the {units}
+keyword; e.g. for {reduced} units the number of chunks may not change
+even if the box size does.
 
 The {bin/1d}, {bin/2d}, and {bin/3d} styles define bins as 1d layers
 (slabs), 2d pencils, or 3d boxes.  The {dim}, {origin}, and {delta}
@@ -386,7 +388,7 @@ If {compress yes} is set, and the {compress} keyword comes before the
 {limit} keyword, the compression operation is performed first, as
 described below, which resets {Nchunk}.  The {limit} keyword is then
 applied to the new {Nchunk} value, exactly as described in the
-preceeding paragraph.  Note that in this case, all atoms will end up
+preceding paragraph.  Note that in this case, all atoms will end up
 with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or
 compute/fix/variable value) may have been > {Nc}, because of the
 compression operation.
@@ -459,7 +461,7 @@ The original chunk IDs (before renumbering) can be accessed by the
 which outputs the original IDs as one of the columns in its global
 output array.  For example, using the "compute cluster/atom" command
 discussed above, the original 5 unique chunk IDs might be atom IDs
-(27,4982,58374,857838,1000000).  After compresion, these will be
+(27,4982,58374,857838,1000000).  After compression, these will be
 renumbered to (1,2,3,4,5).  The original values (27,...,1000000) can
 be output to a file by the "fix ave/chunk"_fix_ave_chunk.html command,
 or by using the "fix ave/time"_fix_ave_time.html command in
@@ -538,7 +540,7 @@ is set to {yes}, an out-of-domain atom will have its chunk ID set to
 to the first or last bin in both the radial and axis dimensions.  If
 {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
+dimension, 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
 dimension.  This is the case if the {bound} keyword settings are
 {lower} and {upper}, which is the default.  If the {bound} keyword

doc/src/compute_cna_atom.txt

@@ -42,7 +42,7 @@ performed on mono-component systems.
 
 The CNA calculation can be sensitive to the specified cutoff value.
 You should insure the appropriate nearest neighbors of an atom are
-found within the cutoff distance for the presumed crystal strucure.
+found within the cutoff distance for the presumed crystal structure.
 E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
 neighbors for perfect BCC crystals.  These formulas can be used to
 obtain a good cutoff distance:

doc/src/compute_com.txt

@@ -25,7 +25,7 @@ Define a computation that calculates the center-of-mass of the group
 of atoms, including all effects due to atoms passing thru periodic
 boundaries.
 
-A vector of three quantites is calculated by this compute, which
+A vector of three quantities is calculated by this compute, which
 are the x,y,z coordinates of the center of mass.
 
 NOTE: The coordinates of an atom contribute to the center-of-mass in

doc/src/compute_coord_atom.txt

@@ -64,13 +64,13 @@ defined by the orientational order parameter calculated by the
 "compute orientorder/atom"_compute_orientorder_atom.html command.
 This {cstyle} thus allows one to apply the ten Wolde's criterion to
 identify crystal-like atoms in a system, as discussed in "ten
-Wolde"_#tenWolde.
+Wolde"_#tenWolde1.
 
 The ID of the previously specified "compute
 orientorder/atom"_compute_orientorder/atom command is specified as
 {orientorderID}.  The compute must invoke its {components} option to
 calculate components of the {Ybar_lm} vector for each atoms, as
-described in its documenation.  Note that orientorder/atom compute
+described in its documentation.  Note that orientorder/atom compute
 defines its own criteria for identifying neighboring atoms.  If the
 scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
 orientorder/atom compute is larger than the specified {threshold},
@@ -127,6 +127,6 @@ explained above.
 
 :line
 
-:link(tenWolde)
+:link(tenWolde1)
 [(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
 J. Chem. Phys. 104, 9932 (1996).

doc/src/compute_damage_atom.txt

@@ -47,7 +47,7 @@ any command that uses per-atom values from a compute as input.  See
 "Section 6.15"_Section_howto.html#howto_15 for an overview of
 LAMMPS output options.
 
-The per-atom vector values are unitlesss numbers (damage) >= 0.0.
+The per-atom vector values are unitless numbers (damage) >= 0.0.
 
 [Restrictions:]
 

doc/src/compute_dilatation_atom.txt

@@ -50,7 +50,7 @@ This compute calculates a per-atom vector, which can be accessed by
 any command that uses per-atom values from a compute as input. See
 Section_howto 15 for an overview of LAMMPS output options.
 
-The per-atom vector values are unitlesss numbers (theta) >= 0.0.
+The per-atom vector values are unitless numbers (theta) >= 0.0.
 
 [Restrictions:]
 

doc/src/compute_displace_atom.txt

@@ -25,7 +25,7 @@ Define a computation that calculates the current displacement of each
 atom in the group from its original coordinates, including all effects
 due to atoms passing thru periodic boundaries.
 
-A vector of four quantites per atom is calculated by this compute.
+A vector of four quantities per atom is calculated by this compute.
 The first 3 elements of the vector are the dx,dy,dz displacements.
 The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
 dz*dz).

doc/src/compute_dpd.txt

@@ -64,7 +64,7 @@ command.
 
 :line
 
-:link(Larentzos)
+:link(Larentzos1)
 [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
 W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
 Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research

doc/src/compute_dpd_atom.txt

@@ -59,7 +59,7 @@ command.
 
 :line
 
-:link(Larentzos)
+:link(Larentzos2)
 [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
 W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
 Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research

doc/src/compute_event_displace.txt

@@ -14,7 +14,7 @@ compute ID group-ID event/displace threshold :pre
 
 ID, group-ID are documented in "compute"_compute.html command
 event/displace = style name of this compute command
-threshold = minimum distance anyparticle must move to trigger an event (distance units) :ul
+threshold = minimum distance any particle must move to trigger an event (distance units) :ul
 
 [Examples:]
 
@@ -37,7 +37,7 @@ further than the threshold distance.
 NOTE: If the system is undergoing significant center-of-mass motion,
 due to thermal motion, an external force, or an initial net momentum,
 then this compute will not be able to distinguish that motion from
-local atom displacements and may generate "false postives."
+local atom displacements and may generate "false positives."
 
 [Output info:]
 

doc/src/compute_global_atom.txt

@@ -55,7 +55,7 @@ M is the actual length of the input vector, then an output value of
 0.0 is assigned to the atom.
 
 An example of how this command is useful, is in the context of
-"chunks" which are static or dyanmic subsets of atoms.  The "compute
+"chunks" which are static or dynamic subsets of atoms.  The "compute
 chunk/atom"_compute_chunk_atom.html command assigns unique chunk IDs
 to each atom.  It's output can be used as the {index} parameter for
 this command.  Various other computes with "chunk" in their style
@@ -192,7 +192,7 @@ reference thermodynamic keywords and various other attributes of
 atoms, or invoke other computes, fixes, or variables when they are
 evaluated, so this is a very general means of generating a vector of
 global quantities which the {index} parameter will reference for
-assignement of global values to atoms.
+assignment of global values to atoms.
 
 :line
 
@@ -207,7 +207,7 @@ See "Section 6.15"_Section_howto.html#howto_15 for an overview of
 LAMMPS output options.
 
 The per-atom vector or array values will be in whatever units the
-corresponsing input values are in.
+corresponding input values are in.
 
 [Restrictions:] none
 

doc/src/compute_group_group.txt

@@ -16,10 +16,11 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
 group/group = style name of this compute command :l
 group2-ID = group ID of second (or same) group :l
 zero or more keyword/value pairs may be appended :l
-keyword = {pair} or {kspace} or {boundary} :l
+keyword = {pair} or {kspace} or {boundary} or {molecule} :l
   {pair} value = {yes} or {no}
   {kspace} value = {yes} or {no}
-  {boundary} value = {yes} or {no} :pre
+  {boundary} value = {yes} or {no}
+  {molecule} value = {off} or {inter} or {intra} :pre
 :ule
 
 [Examples:]
@@ -46,6 +47,13 @@ NOTE: The energies computed by the {pair} keyword do not include tail
 corrections, even if they are enabled via the
 "pair_modify"_pair_modify.html command.
 
+If the {molecule} keyword is set to {inter} or {intra} than an
+additional check is made based on the molecule IDs of the two atoms in
+each pair before including their pairwise interaction energy and
+force.  For the {inter} setting, the two atoms must be in different
+molecules.  For the {intra} setting, the two atoms must be in the same
+molecule.
+
 If the {kspace} keyword is set to {yes}, which is not the default, and
 if a "kspace_style"_kspace_style.html is defined, then the interaction
 energy will include a Kspace component which is the long-range
@@ -66,6 +74,10 @@ affect the force calculation and will be zero if one or both of the
 groups are charge neutral.  This energy correction term is the same as
 that included in the regular Ewald and PPPM routines.
 
+NOTE: The {molecule} setting only affects the group/group
+contributions calculated by the {pair} keyword.  It does not affect
+the group/group contributions calculated by the {kspace} keyword.
+
 This compute does not calculate any bond or angle or dihedral or
 improper interactions between atoms in the two groups.
 
@@ -78,6 +90,22 @@ work (FFTs, Ewald summation) as computing long-range forces for the
 entire system.  Thus it can be costly to invoke this compute too
 frequently.
 
+NOTE: If you have a bonded system, then the settings of
+"special_bonds"_special_bonds.html command can remove pairwise
+interactions between atoms in the same bond, angle, or dihedral.  This
+is the default setting for the "special_bonds"_special_bonds.html
+command, and means those pairwise interactions do not appear in the
+neighbor list.  Because this compute uses a neighbor list, it also
+means those pairs will not be included in the group/group interaction.
+This does not apply when using long-range coulomb interactions
+({coul/long}, {coul/msm}, {coul/wolf} or similar.  One way to get
+around this would be to set special_bond scaling factors to very tiny
+numbers that are not exactly zero (e.g. 1.0e-50). Another workaround
+is to write a dump file, and use the "rerun"_rerun.html command to
+compute the group/group interactions for snapshots in the dump file.
+The rerun script can use a "special_bonds"_special_bonds.html command
+that includes all pairs in the neighbor list.
+
 If you desire a breakdown of the interactions into a pairwise and
 Kspace component, simply invoke the compute twice with the appropriate
 yes/no settings for the {pair} and {kspace} keywords.  This is no more
@@ -119,7 +147,8 @@ The {ewald} and {pppm} styles do.
 
 [Default:]
 
-The option defaults are pair = yes, kspace = no, and boundary = yes.
+The option defaults are pair = yes, kspace = no, boundary = yes,
+molecule = off.
 
 :line
 

doc/src/compute_heat_flux.txt

@@ -38,7 +38,7 @@ subtracted to a group of atoms.
 The compute takes three arguments which are IDs of other
 "computes"_compute.html.  One calculates per-atom kinetic energy
 ({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the
-third calcualtes per-atom stress ({stress-ID}).
+third calculates per-atom stress ({stress-ID}).
 
 NOTE: These other computes should provide values for all the atoms in
 the group this compute specifies.  That means the other computes could
@@ -83,7 +83,7 @@ The heat flux can be output every so many timesteps (e.g. via the
 post-processing operation, an autocorrelation can be performed, its
 integral estimated, and the Green-Kubo formula above evaluated.
 
-The "fix ave/correlate"_fix_ave_correlate.html command can calclate
+The "fix ave/correlate"_fix_ave_correlate.html command can calculate
 the autocorrelation.  The trap() function in the
 "variable"_variable.html command can calculate the integral.
 

doc/src/compute_inertia_chunk.txt

@@ -35,7 +35,7 @@ chunk/atom"_compute_chunk_atom.html doc page and "Section
 defined and examples of how they can be used to measure properties of
 a system.
 
-This compute calculates the 6 components of the symmetric intertia
+This compute calculates the 6 components of the symmetric inertia
 tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz.  The
 calculation includes all effects due to atoms passing thru periodic
 boundaries.

doc/src/compute_modify.txt

@@ -14,27 +14,29 @@ compute_modify compute-ID keyword value ... :pre
 
 compute-ID = ID of the compute to modify :ulb,l
 one or more keyword/value pairs may be listed :l
-keyword = {extra} or {dynamic} :l
-  {extra} value = N
+keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l
+  {extra/dof} value = N
     N = # of extra degrees of freedom to subtract
-  {dynamic} value = {yes} or {no}
-    yes/no = do or do not recompute the number of atoms contributing to the temperature :pre
+  {extra} syntax is identical to {extra/dof}, will be disabled at some point
+  {dynamic/dof} value = {yes} or {no}
+    yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
+  {dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre
 :ule
 
 [Examples:]
 
-compute_modify myTemp extra 0
-compute_modify newtemp dynamic yes extra 600 :pre
+compute_modify myTemp extra/dof 0
+compute_modify newtemp dynamic/dof yes extra/dof 600 :pre
 
 [Description:]
 
 Modify one or more parameters of a previously defined compute.  Not
 all compute styles support all parameters.
 
-The {extra} keyword refers to how many degrees-of-freedom are
-subtracted (typically from 3N) as a normalizing factor in a
-temperature computation.  Only computes that compute a temperature use
-this option.  The default is 2 or 3 for "2d or 3d
+The {extra/dof} or {extra} keyword refers to how many
+degrees-of-freedom are subtracted (typically from 3N) as a normalizing
+factor in a temperature computation.  Only computes that compute a
+temperature use this option.  The default is 2 or 3 for "2d or 3d
 systems"_dimension.html which is a correction factor for an ensemble
 of velocities with zero total linear momentum. For compute
 temp/partial, if one or more velocity components are excluded, the
@@ -43,14 +45,21 @@ number for the {extra} parameter if you need to add
 degrees-of-freedom.  See the "compute
 temp/asphere"_compute_temp_asphere.html command for an example.
 
-The {dynamic} keyword determines whether the number of atoms N in the
-compute group is re-computed each time a temperature is computed.
-Only compute styles that calculate a temperature use this option.  By
-default, N is assumed to be constant.  If you are adding atoms to the
-system (see the "fix pour"_fix_pour.html or "fix
-deposit"_fix_deposit.html commands) or expect atoms to be lost
-(e.g. due to evaporation), then this option should be used to insure
-the temperature is correctly normalized.
+The {dynamic/dof} or {dynamic} keyword determines whether the number
+of atoms N in the compute group and their associated degrees of
+freedom are re-computed each time a temperature is computed.  Only
+compute styles that calculate a temperature use this option.  By
+default, N and their DOF are assumed to be constant.  If you are
+adding atoms or molecules to the system (see the "fix
+pour"_fix_pour.html, "fix deposit"_fix_deposit.html, and "fix
+gcmc"_fix_gcmc.html commands) or expect atoms or molecules to be lost
+(e.g. due to exiting the simulation box or via "fix
+evaporate"_fix_evaporate.html), then this option should be used to
+insure the temperature is correctly normalized.
+
+NOTE: The {extra} and {dynamic} keywords should not be used as they
+are deprecated (March 2017) and will eventually be disabled.  Instead,
+use the equivalent {extra/dof} and {dynamic/dof} keywords.
 
 [Restrictions:] none
 
@@ -60,5 +69,5 @@ the temperature is correctly normalized.
 
 [Default:]
 
-The option defaults are extra = 2 or 3 for 2d or 3d systems and
-dynamic = no.
+The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and
+dynamic/dof = no.

doc/src/compute_msd.txt

@@ -33,7 +33,7 @@ passing thru periodic boundaries.  For computation of the non-Gaussian
 parameter of mean-squared displacement, see the "compute
 msd/nongauss"_compute_msd_nongauss.html command.
 
-A vector of four quantites is calculated by this compute.  The first 3
+A vector of four quantities is calculated by this compute.  The first 3
 elements of the vector are the squared dx,dy,dz displacements, summed
 and averaged over atoms in the group.  The 4th element is the total
 squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and

doc/src/compute_msd_chunk.txt

@@ -35,7 +35,7 @@ chunk/atom"_compute_chunk_atom.html doc page and "Section
 defined and examples of how they can be used to measure properties of
 a system.
 
-Four quantites are calculated by this compute for each chunk.  The
+Four quantities are calculated by this compute for each chunk.  The
 first 3 quantities are the squared dx,dy,dz displacements of the
 center-of-mass.  The 4th component is the total squared displacement,
 i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass.  These

doc/src/compute_msd_nongauss.txt

@@ -30,12 +30,12 @@ Define a computation that calculates the mean-squared displacement
 (MSD) and non-Gaussian parameter (NGP) of the group of atoms,
 including all effects due to atoms passing thru periodic boundaries.
 
-A vector of three quantites is calculated by this compute.  The first
+A vector of three quantities is calculated by this compute.  The first
 element of the vector is the total squared dx,dy,dz displacements
 drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the
 fourth power of these displacements drfourth = (dx*dx + dy*dy +
 dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the
-group.  The 3rd component is the nonGaussian diffusion paramter NGP =
+group.  The 3rd component is the nonGaussian diffusion parameter NGP =
 3*drfourth/(5*drsquared*drsquared), i.e.
 
 :c,image(Eqs/compute_msd_nongauss.jpg)
@@ -48,7 +48,7 @@ others.
 
 If the {com} option is set to {yes} then the effect of any drift in
 the center-of-mass of the group of atoms is subtracted out before the
-displacment of each atom is calcluated.
+displacment of each atom is calculated.
 
 See the "compute msd"_compute_msd.html doc page for further important
 NOTEs, which also apply to this compute.

doc/src/compute_orientorder_atom.txt

@@ -78,7 +78,7 @@ normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
 explicitly included in the keyword {degrees}. This option can be used
 in conjunction with "compute coord_atom"_compute_coord_atom.html to
 calculate the ten Wolde's criterion to identify crystal-like
-particles, as discussed in "ten Wolde"_#tenWolde.
+particles, as discussed in "ten Wolde"_#tenWolde2.
 
 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
@@ -143,6 +143,6 @@ Phys. Rev. B 28, 784 (1983).
 [(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke,
 J. Chem. Phys. 138, 044501 (2013).
 
-:link(tenWolde)
+:link(tenWolde2)
 [(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
 J. Chem. Phys. 104, 9932 (1996).

doc/src/compute_pair.txt

@@ -43,7 +43,7 @@ style van der Waals interaction or not) is tallied in {evdwl}.  If
 as a global scalar by this compute.  This is useful when using
 "pair_style hybrid"_pair_hybrid.html if you want to know the portion
 of the total energy contributed by one sub-style.  If {evalue} is
-specfied as {evdwl} or {ecoul}, then just that portion of the energy
+specified as {evdwl} or {ecoul}, then just that portion of the energy
 is stored as a global scalar.
 
 NOTE: The energy returned by the {evdwl} keyword does not include tail
@@ -52,7 +52,7 @@ corrections, even if they are enabled via the
 
 Some pair styles tally additional quantities, e.g. a breakdown of
 potential energy into a dozen or so components is tallied by the
-"pair_style reax"_pair_reax.html commmand.  These values (1 or more)
+"pair_style reax"_pair_reax.html command.  These values (1 or more)
 are stored as a global vector by this compute.  See the doc page for
 "individual pair styles"_pair_style.html for info on these values.
 

doc/src/compute_pair_local.txt

@@ -47,7 +47,7 @@ force cutoff distance for that interaction, as defined by the
 "pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html
 commands.
 
-The value {dist} is the distance bewteen the pair of atoms.
+The value {dist} is the distance between the pair of atoms.
 
 The value {eng} is the interaction energy for the pair of atoms.
 

doc/src/compute_pe_atom.txt

@@ -49,9 +49,9 @@ pairwise interactions between 1-4 atoms.  The energy contribution of
 these terms is included in the pair energy, not the dihedral energy.
 
 The KSpace contribution is calculated using the method in
-"(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
+"(Heyes)"_#Heyes1 for the Ewald method and a related method for PPPM,
 as specified by the "kspace_style pppm"_kspace_style.html command.
-For PPPM, the calcluation requires 1 extra FFT each timestep that
+For PPPM, the calculation requires 1 extra FFT each timestep that
 per-atom energy is calculated.  This "document"_PDF/kspace.pdf
 describes how the long-range per-atom energy calculation is performed.
 
@@ -97,5 +97,5 @@ stress/atom"_compute_stress_atom.html
 
 :line
 
-:link(Heyes)
+:link(Heyes1)
 [(Heyes)] Heyes, Phys Rev B 49, 755 (1994),

doc/src/compute_plasticity_atom.txt

@@ -44,7 +44,7 @@ This compute calculates a per-atom vector, which can be accessed by
 any command that uses per-atom values from a compute as input. See
 Section_howto 15 for an overview of LAMMPS output options.
 
-The per-atom vector values are unitlesss numbers (lambda) >= 0.0.
+The per-atom vector values are unitless numbers (lambda) >= 0.0.
 
 [Restrictions:]
 

doc/src/compute_pressure.txt

@@ -70,7 +70,7 @@ means include all terms except the kinetic energy {ke}.
 Details of how LAMMPS computes the virial efficiently for the entire
 system, including for manybody potentials and accounting for the
 effects of periodic boundary conditions are discussed in
-"(Thompson)"_#Thompson.
+"(Thompson)"_#Thompson1.
 
 The temperature and kinetic energy tensor is not calculated by this
 compute, but rather by the temperature compute specified with the
@@ -89,7 +89,7 @@ commands"_compute.html to determine which ones include a bias.
 
 Also note that the N in the first formula above is really
 degrees-of-freedom divided by d = dimensionality, where the DOF value
-is calcluated by the temperature compute.  See the various "compute
+is calculated by the temperature compute.  See the various "compute
 temperature"_compute.html styles for details.
 
 A compute of this style with the ID of "thermo_press" is created when
@@ -150,5 +150,5 @@ stress/atom"_compute_stress_atom.html,
 
 :line
 
-:link(Thompson)
+:link(Thompson1)
 [(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).

doc/src/compute_property_chunk.txt

@@ -64,7 +64,7 @@ can only be used if the {compress} keyword was set to {yes} for the
 "compute chunk/atom"_compute_chunk_atom.html command referenced by
 chunkID.  This means that the original chunk IDs (e.g. molecule IDs)
 will have been compressed to remove chunk IDs with no atoms assigned
-to them.  Thus a compresed chunk ID of 3 may correspond to an original
+to them.  Thus a compressed chunk ID of 3 may correspond to an original
 chunk ID (molecule ID in this case) of 415.  The {id} attribute will
 then be 415 for the 3rd chunk.
 

doc/src/compute_rdf.txt

@@ -10,21 +10,27 @@ compute rdf command :h3
 
 [Syntax:]
 
-compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... :pre
+compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... keyword/value ... :pre
 
-ID, group-ID are documented in "compute"_compute.html command
-rdf = style name of this compute command
-Nbin = number of RDF bins
-itypeN = central atom type for Nth RDF histogram (see asterisk form below)
-jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+rdf = style name of this compute command :l
+Nbin = number of RDF bins :l
+itypeN = central atom type for Nth RDF histogram (see asterisk form below) :l
+jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) :l
+
+zero or more keyword/value pairs may be appended :l
+keyword = {cutoff} :l
+  {cutoff} value = Rcut
+    Rcut = cutoff distance for RDF computation (distance units) :pre
+:ule
 
 [Examples:]
 
 compute 1 all rdf 100
 compute 1 all rdf 100 1 1
-compute 1 all rdf 100 * 3
+compute 1 all rdf 100 * 3 cutoff 5.0
 compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
-compute 1 fluid rdf 500 1*3 2 5 *10 :pre
+compute 1 fluid rdf 500 1*3 2 5 *10 cutoff 3.5 :pre
 
 [Description:]
 
@@ -32,7 +38,8 @@ Define a computation that calculates the radial distribution function
 (RDF), also called g(r), and the coordination number for a group of
 particles.  Both are calculated in histogram form by binning pairwise
 distances into {Nbin} bins from 0.0 to the maximum force cutoff
-defined by the "pair_style"_pair_style.html command.  The bins are of
+defined by the "pair_style"_pair_style.html command or the cutoff
+distance {Rcut} specified via the {cutoff} keyword.  The bins are of
 uniform size in radial distance.  Thus a single bin encompasses a thin
 shell of distances in 3d and a thin ring of distances in 2d.
 
@@ -41,17 +48,41 @@ NOTE: If you have a bonded system, then the settings of
 interactions between atoms in the same bond, angle, or dihedral.  This
 is the default setting for the "special_bonds"_special_bonds.html
 command, and means those pairwise interactions do not appear in the
-neighbor list.  Because this fix uses the neighbor list, it also means
+neighbor list.  Because this fix uses a neighbor list, it also means
 those pairs will not be included in the RDF. This does not apply when
-using long-range coulomb ({coul/long}, {coul/msm}, {coul/wolf} or
-similar.  One way to get around this would be to set special_bond
-scaling factors to very tiny numbers that are not exactly zero
-(e.g. 1.0e-50). Another workaround is to write a dump file, and use
-the "rerun"_rerun.html command to compute the RDF for snapshots in the
-dump file.  The rerun script can use a
+using long-range coulomb interactions ({coul/long}, {coul/msm},
+{coul/wolf} or similar.  One way to get around this would be to set
+special_bond scaling factors to very tiny numbers that are not exactly
+zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
+use the "rerun"_rerun.html command to compute the RDF for snapshots in
+the dump file.  The rerun script can use a
 "special_bonds"_special_bonds.html command that includes all pairs in
 the neighbor list.
 
+By default the RDF is computed out to the maximum force cutoff defined
+by the "pair_style"_pair_style.html command.  If the {cutoff} keyword
+is used, then the RDF is computed accurately out to the {Rcut} > 0.0
+distance specified.
+
+NOTE: Normally, you should only use the {cutoff} keyword if no pair
+style is defined, e.g. the "rerun"_rerun.html command is being used to
+post-process a dump file of snapshots.  Or if you really want the RDF
+for distances beyond the pair_style force cutoff and cannot easily
+post-process a dump file to calculate it.  This is because using the
+{cutoff} keyword incurs extra computation and possibly communication,
+which may slow down your simulation.  If you specify a {Rcut} <= force
+cutoff, you will force an additional neighbor list to be built at
+every timestep this command is invoked (or every reneighboring
+timestep, whichever is less frequent), which is inefficient.  LAMMPS
+will warn you if this is the case.  If you specify a {Rcut} > force
+cutoff, you must insure ghost atom information out to {Rcut} + {skin}
+is communicated, via the "comm_modify cutoff"_comm_modify.html
+command, else the RDF computation cannot be performed, and LAMMPS will
+give an error message.  The {skin} value is what is specified with the
+"neighbor"_neighbor.html command.  In this case, you are forcing a
+large neighbor list to be built just for the RDF computation, and
+extra communication to be performed every timestep.
+
 The {itypeN} and {jtypeN} arguments are optional.  These arguments
 must come in pairs.  If no pairs are listed, then a single histogram
 is computed for g(r) between all atom types.  If one or more pairs are
@@ -153,4 +184,6 @@ change from zero to one at the location of the spike in g(r).
 
 "fix ave/time"_fix_ave_time.html
 
-[Default:] none
+[Default:]
+
+The keyword defaults are cutoff = 0.0 (use the pairwise force cutoff).

doc/src/compute_rigid_local.txt

@@ -123,7 +123,7 @@ The {vx}, {vy}, {vz}, {fx}, {fy}, {fz} attributes are components of
 the COM velocity and force on the COM of the body.
 
 The {omegax}, {omegay}, and {omegaz} attributes are the angular
-velocity componennts of the body around its COM.
+velocity components of the body around its COM.
 
 The {angmomx}, {angmomy}, and {angmomz} attributes are the angular
 momentum components of the body around its COM.

doc/src/compute_saed.txt

@@ -93,7 +93,7 @@ parameters will denote the z1=h, z2=k, and z3=l (in a global since)
 zone axis of an intersecting Ewald sphere.  Diffraction intensities
 will only be computed at the intersection of the reciprocal lattice
 mesh and a {dR_Ewald} thick surface of the Ewald sphere.  See the
-example 3D intestiety data and the intersection of a \[010\] zone axis
+example 3D intensity data and the intersection of a \[010\] zone axis
 in the below image.
 
 :c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg)

doc/src/compute_smd_ulsph_num_neighs.txt

@@ -35,7 +35,7 @@ any command that uses per-particle values from a compute as input.
 See "Section 6.15"_Section_howto.html#howto_15 for an overview of
 LAMMPS output options.
 
-The per-particle values will be given dimentionless, see "units"_units.html.
+The per-particle values will be given dimensionless, see "units"_units.html.
 
 [Restrictions:]
 

doc/src/compute_sna_atom.txt

@@ -24,7 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l
 R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l
 w_1, w_2,... = list of neighbor weights, one for each type  :l
 zero or more keyword/value pairs may be appended :l
-keyword = {diagonal} or {rmin0} or {switchflag} :l
+keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag}:l
   {diagonal} value = {0} or {1} or {2} or {3}
      {0} = all j1, j2, j <= twojmax, j2 <= j1
      {1} = subset satisfying j1 == j2
@@ -33,7 +33,13 @@ keyword = {diagonal} or {rmin0} or {switchflag} :l
   {rmin0} value = parameter in distance to angle conversion (distance units)
   {switchflag} value = {0} or {1}
      {0} = do not use switching function
-     {1} = use switching function :pre
+     {1} = use switching function
+  {bzeroflag} value = {0} or {1}
+     {0} = do not subtract B0
+     {1} = subtract B0
+  {quadraticflag} value = {0} or {1}
+     {0} = do not generate quadratic terms
+     {1} = generate quadratic terms :pre
 :ule
 
 [Examples:]
@@ -50,12 +56,12 @@ for each atom in a group.
 Bispectrum components of an atom are order parameters characterizing
 the radial and angular distribution of neighbor atoms. The detailed
 mathematical definition is given in the paper by Thompson et
-al. "(Thompson)"_#Thompson2014
+al. "(Thompson)"_#Thompson20141
 
 The position of a neighbor atom {i'} relative to a central atom {i} is
 a point within the 3D ball of radius {R_ii' = rcutfac*(R_i + R_i')}
 
-Bartok et al. "(Bartok)"_#Bartok2010, proposed mapping this 3D ball
+Bartok et al. "(Bartok)"_#Bartok20101, proposed mapping this 3D ball
 onto the 3-sphere, the surface of the unit ball in a four-dimensional
 space.  The radial distance {r} within {R_ii'} is mapped on to a third
 polar angle {theta0} defined by,
@@ -92,7 +98,7 @@ The expansion coefficients {u^j_m,m'} are complex-valued and they are
 not directly useful as descriptors, because they are not invariant
 under rotation of the polar coordinate frame. However, the following
 scalar triple products of expansion coefficients can be shown to be
-real-valued and invariant under rotation "(Bartok)"_#Bartok2010.
+real-valued and invariant under rotation "(Bartok)"_#Bartok20101.
 
 :c,image(Eqs/compute_sna_atom3.jpg)
 
@@ -148,11 +154,25 @@ linear mapping from radial distance to polar angle {theta0} on the
 The argument {twojmax} and the keyword {diagonal} define which
 bispectrum components are generated. See section below on output for a
 detailed explanation of the number of bispectrum components and the
-ordered in which they are listed
+ordered in which they are listed.
 
 The keyword {switchflag} can be used to turn off the switching
 function.
 
+The keyword {bzeroflag} determines whether or not {B0}, the bispectrum
+components of an atom with no neighbors, are subtracted from
+the calculated bispectrum components. This optional keyword is only
+available for compute {sna/atom}, as {snad/atom} and {snav/atom}
+are unaffected by the removal of constant terms.
+
+The keyword {quadraticflag} determines whether or not the
+quadratic analogs to the bispectrum quantities are generated.
+These are formed by taking the outer product of the vector
+of bispectrum components with itself.
+See section below on output for a
+detailed explanation of the number of quadratic terms and the
+ordered in which they are listed.
+
 NOTE: If you have a bonded system, then the settings of
 "special_bonds"_special_bonds.html command can remove pairwise
 interactions between atoms in the same bond, angle, or dihedral.  This
@@ -171,7 +191,7 @@ command that includes all pairs in the neighbor list.
 
 Compute {sna/atom} calculates a per-atom array, each column
 corresponding to a particular bispectrum component.  The total number
-of columns and the identities of the bispectrum component contained in
+of columns and the identity of the bispectrum component contained in
 each column depend on the values of {twojmax} and {diagonal}, as
 described by the following piece of python code:
 
@@ -204,6 +224,19 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz},
 notation.  Each of these sub-blocks contains one column for each
 bispectrum component, the same as for compute {sna/atom}
 
+For example, if {K}=30 and ntypes=1, the number of columns in the per-atom
+arrays generated by {sna/atom}, {snad/atom}, and {snav/atom}
+are 30, 90, and 180, respectively. With {quadratic} value=1,
+the numbers of columns are 930, 2790, and 5580, respectively.
+
+If the {quadratic} keyword value is set to 1, then additional
+columns are appended to each per-atom array, corresponding to
+a matrix of quantities that are products of two bispectrum components. If the
+number of bispectrum components is {K}, then the number of matrix elements
+is {K}^2. These are output in subblocks of {K}^2 columns, using the same
+ordering of columns and sub-blocks as was used for the bispectrum
+components.
+
 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
@@ -222,15 +255,15 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 [Default:]
 
 The optional keyword defaults are {diagonal} = 0, {rmin0} = 0,
-{switchflag} = 1.
+{switchflag} = 1, {bzeroflag} = 1, {quadraticflag} = 0,
 
 :line
 
-:link(Thompson2014)
+:link(Thompson20141)
 [(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
 available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880
 
-:link(Bartok2010)
+:link(Bartok20101)
 [(Bartok)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
 
 :link(Meremianin2006)

doc/src/compute_stress_atom.txt

@@ -74,7 +74,7 @@ other atoms in the simulation, not just with other atoms in the group.
 
 Details of how LAMMPS computes the virial for individual atoms for
 either pairwise or manybody potentials, and including the effects of
-periodic boundary conditions is discussed in "(Thompson)"_#Thompson.
+periodic boundary conditions is discussed in "(Thompson)"_#Thompson2.
 The basic idea for manybody potentials is to treat each component of
 the force computation between a small cluster of atoms in the same
 manner as in the formula above for bond, angle, dihedral, etc
@@ -89,10 +89,10 @@ pairwise interactions between 1-4 atoms.  The virial contribution of
 these terms is included in the pair virial, not the dihedral virial.
 
 The KSpace contribution is calculated using the method in
-"(Heyes)"_#Heyes for the Ewald method and by the methodology described
-in "(Sirk)"_#Sirk for PPPM.  The choice of KSpace solver is specified
+"(Heyes)"_#Heyes2 for the Ewald method and by the methodology described
+in "(Sirk)"_#Sirk1 for PPPM.  The choice of KSpace solver is specified
 by the "kspace_style pppm"_kspace_style.html command.  Note that for
-PPPM, the calcluation requires 6 extra FFTs each timestep that
+PPPM, the calculation requires 6 extra FFTs each timestep that
 per-atom stress is calculated.  Thus it can significantly increase the
 cost of the PPPM calculation if it is needed on a large fraction of
 the simulation timesteps.
@@ -159,11 +159,11 @@ The per-atom array values will be in pressure*volume
 
 :line
 
-:link(Heyes)
+:link(Heyes2)
 [(Heyes)] Heyes, Phys Rev B 49, 755 (1994),
 
-:link(Sirk)
+:link(Sirk1)
 [(Sirk)] Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).
 
-:link(Thompson)
+:link(Thompson2)
 [(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).

doc/src/compute_temp_asphere.txt

@@ -138,7 +138,7 @@ This compute is part of the ASPHERE 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.
 
-This compute requires that atoms store angular momementum and a
+This compute requires that atoms store angular momentum and a
 quaternion as defined by the "atom_style ellipsoid"_atom_style.html
 command.
 

doc/src/compute_temp_body.txt

@@ -120,7 +120,7 @@ This compute is part of the BODY 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.
 
-This compute requires that atoms store angular momementum and a
+This compute requires that atoms store angular momentum and a
 quaternion as defined by the "atom_style body"_atom_style.html
 command.
 

doc/src/compute_temp_chunk.txt

@@ -44,7 +44,7 @@ compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 :pre
 Define a computation that calculates the temperature of a group of
 atoms that are also in chunks, after optionally subtracting out the
 center-of-mass velocity of each chunk.  By specifying optional values,
-it can also calulate the per-chunk temperature or energies of the
+it can also calculate the per-chunk temperature or energies of the
 multiple chunks of atoms.
 
 In LAMMPS, chunks are collections of atoms defined by a "compute
@@ -122,7 +122,7 @@ concept is somewhat ill-defined.  In some cases, you can use the
 {adof} and {cdof} keywords to adjust the calculated degress of freedom
 appropriately, as explained below.
 
-Note that the per-chunk temperature calulated by this compute and the
+Note that the per-chunk temperature calculated by this compute and the
 "fix ave/chunk temp"_fix_ave_chunk.html command can be different.
 This compute calculates the temperature for each chunk for a single
 snapshot.  Fix ave/chunk can do that but can also time average those
@@ -208,7 +208,7 @@ This compute also optionally calculates a global array, if one or more
 of the optional values are specified.  The number of rows in the array
 = the number of chunks {Nchunk} as calculated by the specified
 "compute chunk/atom"_compute_chunk_atom.html command.  The number of
-columns is the number of specifed values (1 or more).  These values
+columns is the number of specified values (1 or more).  These values
 can be accessed by any command that uses global array values from a
 compute as input.  Again, see "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output

doc/src/compute_temp_cs.txt

@@ -27,7 +27,7 @@ compute core_shells all temp/cs cores shells :pre
 Define a computation that calculates the temperature of a system based
 on the center-of-mass velocity of atom pairs that are bonded to each
 other.  This compute is designed to be used with the adiabatic
-core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham.  See
+core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham1.  See
 "Section 6.25"_Section_howto.html#howto_25 of the manual for an
 overview of the model as implemented in LAMMPS.  Specifically, this
 compute enables correct temperature calculation and thermostatting of
@@ -114,6 +114,6 @@ temp/chunk"_compute_temp_chunk.html
 
 :line
 
-:link(MitchellFinchham)
+:link(MitchellFinchham1)
 [(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
 5, 1031-1038 (1993).

doc/src/compute_temp_profile.txt

@@ -43,7 +43,7 @@ atoms, after subtracting out a spatially-averaged center-of-mass
 velocity field, before computing the kinetic energy.  This can be
 useful for thermostatting a collection of atoms undergoing a complex
 flow, e.g. via a profile-unbiased thermostat (PUT) as described in
-"(Evans)"_#Evans.  A compute of this style can be used by any command
+"(Evans)"_#Evans1.  A compute of this style can be used by any command
 that computes a temperature, e.g. "thermo_modify"_thermo_modify.html,
 "fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.
 
@@ -75,7 +75,7 @@ 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
 subtracted to adjust for the removal of the center-of-mass velocity in
-each of Nx*Ny*Nz bins, as discussed in the "(Evans)"_#Evans paper.
+each of Nx*Ny*Nz bins, as discussed in the "(Evans)"_#Evans1 paper.
 
 If the {out} keyword is used with a {tensor} value, which is the
 default, a kinetic energy tensor, stored as a 6-element vector, is
@@ -118,7 +118,7 @@ needed, the subtracted degrees-of-freedom can be altered using the
 
 NOTE: When using the {out} keyword with a value of {bin}, the
 calculated temperature for each bin does not include the
-degrees-of-freedom adjustment described in the preceeding paragraph,
+degrees-of-freedom adjustment described in the preceding paragraph,
 for fixes that constrain molecular motion.  It does include the
 adjustment due to the {extra} option, which is applied to each bin.
 
@@ -126,7 +126,7 @@ See "this howto section"_Section_howto.html#howto_16 of the manual for
 a discussion of different ways to compute temperature and perform
 thermostatting.  Using this compute in conjunction with a
 thermostatting fix, as explained there, will effectively implement a
-profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans.
+profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans1.
 
 [Output info:]
 
@@ -178,5 +178,5 @@ The option default is out = tensor.
 
 :line
 
-:link(Evans)
+:link(Evans1)
 [(Evans)] Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).

doc/src/compute_vacf.txt

@@ -27,7 +27,7 @@ function (VACF), averaged over a group of atoms.  Each atom's
 contribution to the VACF is its current velocity vector dotted into
 its initial velocity vector at the time the compute was specified.
 
-A vector of four quantites is calculated by this compute.  The first 3
+A vector of four quantities is calculated by this compute.  The first 3
 elements of the vector are vx * vx0 (and similarly for the y and z
 components), summed and averaged over atoms in the group.  Vx is the
 current x-component of velocity for the atom, vx0 is the initial

doc/src/compute_voronoi_atom.txt

@@ -217,6 +217,10 @@ This compute is part of the VORONOI 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.
 
+It also requiers you have a copy of the Voro++ library built and
+installed on your system.  See instructions on obtaining and
+installing the Voro++ software in the src/VORONOI/README file.
+
 [Related commands:]
 
 "dump custom"_dump.html, "dump local"_dump.html

doc/src/create_atoms.txt

@@ -101,7 +101,7 @@ positions.
 For the {random} style, N particles are added to the system at
 randomly generated coordinates, which can be useful for generating an
 amorphous system.  The particles are created one by one using the
-speficied random number {seed}, resulting in the same set of particles
+specified random number {seed}, resulting in the same set of particles
 coordinates, independent of how many processors are being used in the
 simulation.  If the {region-ID} argument is specified as NULL, then
 the created particles will be anywhere in the simulation box.  If a
@@ -134,6 +134,17 @@ not overlap existing atoms inappropriately, especially if molecules
 are being added.  The "delete_atoms"_delete_atoms.html command can be
 used to remove overlapping atoms or molecules.
 
+NOTE: You cannot use any of the styles explained above to create atoms
+that are outside the simulation box; they will just be ignored by
+LAMMPS.  This is true even if you are using shrink-wrapped box
+boundaries, as specified by the "boundary"_boundary.html command.
+However, you can first use the "change_box"_change_box.html command to
+temporarily expand the box, then add atoms via create_atoms, then
+finally use change_box command again if needed to re-shrink-wrap the
+new atoms.  See the "change_box"_change_box.html doc page for an
+example of how to do this, using the create_atoms {single} style to
+insert a new atom outside the current simulation box.
+
 :line
 
 Individual atoms are inserted by this command, unless the {mol}

doc/src/dihedral_charmm.txt

@@ -10,21 +10,25 @@ dihedral_style charmm command :h3
 dihedral_style charmm/intel command :h3
 dihedral_style charmm/kk command :h3
 dihedral_style charmm/omp command :h3
+dihedral_style charmmfsw command :h3
 
 [Syntax:]
 
-dihedral_style charmm :pre
+dihedral_style style :pre
+
+style = {charmm} or {charmmfsw} :ul
 
 [Examples:]
 
 dihedral_style charmm
+dihedral_style charmmfsw
 dihedral_coeff  1 0.2 1 180 1.0
 dihedral_coeff  2 1.8 1   0 1.0
 dihedral_coeff  1 3.1 2 180 0.5 :pre
 
 [Description:]
 
-The {charmm} dihedral style uses the potential
+The {charmm} and {charmmfsw} dihedral styles use the potential
 
 :c,image(Eqs/dihedral_charmm.jpg)
 
@@ -34,6 +38,16 @@ field (see comment on weighting factors below).  See
 "(Cornell)"_#dihedral-Cornell for a description of the AMBER force
 field.
 
+NOTE: The newer {charmmfsw} style was released in March 2017.  We
+recommend it be used instead of the older {charmm} style when running
+a simulation with the CHARMM force field, either with long-range
+Coulombics or a Coulomb cutoff, via the "pair_style
+lj/charmmfsw/coul/long"_pair_charmm.html and "pair_style
+lj/charmmfsw/coul/charmmfsh"_pair_charmm.html commands respectively.
+Otherwise the older {charmm} style is fine to use.  See the discussion
+below and more details on the "pair_style charmm"_pair_charmm.html doc
+page.
+
 The following coefficients must be defined for each dihedral type via the
 "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
@@ -73,13 +87,29 @@ special_bonds 1-4 scaling factor to 0.0 (which is the
 default). Otherwise 1-4 non-bonded interactions in dihedrals will be
 computed twice.
 
-Also note that for AMBER force fields, which use pair styles with
-"lj/cut", the special_bonds 1-4 scaling factor should be set to the
-AMBER defaults (1/2 and 5/6) and all the dihedral weighting factors
-(4th coeff above) must be set to 0.0. In this case, you can use any
-pair style you wish, since the dihedral does not need any
-Lennard-Jones parameter information and will not compute any 1-4
-non-bonded interactions.
+For simulations using the CHARMM force field with a Coulomb cutoff,
+the difference between the {charmm} and {charmmfsw} styles is in the
+computation of the 1-4 non-bond interactions, though only if the
+distance between the two atoms is within the switching region of the
+pairwise potential defined by the corresponding CHARMM pair style,
+i.e. within the outer cutoff specified for the pair style.  The
+{charmmfsw} style should only be used when using the corresponding
+"pair_style lj/charmmfsw/coul/charmmfsw"_pair_charmm.html or
+"pair_style lj/charmmfsw/coul/long"_pair_charmm.html commands.  Use
+the {charmm} style with the older "pair_style"_pair_charmm.html
+commands that have just "charmm" in their style name.  See the
+discussion on the "CHARMM pair_style"_pair_charmm.html doc page for
+details.
+
+Note that for AMBER force fields, which use pair styles with "lj/cut",
+the special_bonds 1-4 scaling factor should be set to the AMBER
+defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
+coeff above) must be set to 0.0. In this case, you can use any pair
+style you wish, since the dihedral does not need any Lennard-Jones
+parameter information and will not compute any 1-4 non-bonded
+interactions.  Likewise the {charmm} or {charmmfsw} styles are
+identical in this case since no 1-4 non-bonded interactions are
+computed.
 
 :line
 

doc/src/dihedral_class2.txt

@@ -8,6 +8,7 @@
 
 dihedral_style class2 command :h3
 dihedral_style class2/omp command :h3
+dihedral_style class2/kk command :h3
 
 [Syntax:]
 

doc/src/dihedral_hybrid.txt

@@ -82,7 +82,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 Unlike other dihedral styles, the hybrid dihedral style does not store
 dihedral coefficient info for individual sub-styles in a "binary
-restart files"_restart.html.  Thus when retarting a simulation from a
+restart files"_restart.html.  Thus when restarting a simulation from a
 restart file, you need to re-specify dihedral_coeff commands.
 
 [Related commands:]

doc/src/dump.txt

@@ -7,12 +7,12 @@
 :line
 
 dump command :h3
-"dump custom/vtk"_dump_custom_vtk.html command :h3
+"dump vtk"_dump_vtk.html command :h3
 "dump h5md"_dump_h5md.html command :h3
+"dump molfile"_dump_molfile.html command :h3
+"dump netcdf"_dump_netcdf.html 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:]
 
@@ -20,7 +20,7 @@ dump ID group-ID style N file args :pre
 
 ID = user-assigned name for the dump :ulb,l
 group-ID = ID of the group of atoms to be dumped :l
-style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {dcd} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} or {h5md} or {image} or {movie} or {molfile} or {local} or {custom} or {custom/gz} or {custom/mpiio} :l
+style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
 N = dump every this many timesteps :l
 file = name of file to write dump info to :l
 args = list of arguments for a particular style :l
@@ -30,33 +30,22 @@ args = list of arguments for a particular style :l
   {cfg} args = same as {custom} args, see below
   {cfg/gz} args = same as {custom} args, see below
   {cfg/mpiio} args = same as {custom} args, see below
+  {custom}, {custom/gz}, {custom/mpiio} args = see below
   {dcd} args = none
+  {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page
+  {image} args = discussed on "dump image"_dump_image.html doc page
+  {local} args = see below
+  {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page
+  {movie} args = discussed on "dump image"_dump_image.html doc page
+  {netcdf} args = discussed on "dump netcdf"_dump_netcdf.html doc page
+  {netcdf/mpiio} args = discussed on "dump netcdf"_dump_netcdf.html doc page
+  {vtk} args = same as {custom} args, see below, also "dump vtk"_dump_vtk.html doc page
   {xtc} args = none
-  {xyz} args = none :pre
-  {xyz/gz} args = none :pre
+  {xyz} args = none
+  {xyz/gz} args = none
   {xyz/mpiio} args = none :pre
 
-  {custom/vtk} args = similar to custom args below, discussed on "dump custom/vtk"_dump_custom_vtk.html doc page :pre
-
-  {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page :pre
-
-  {image} args = discussed on "dump image"_dump_image.html doc page :pre
-
-  {movie} args = discussed on "dump image"_dump_image.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\[I\]
-      index = enumeration of local values
-      c_ID = local vector calculated by a compute with ID
-      c_ID\[I\] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
-      f_ID = local vector calculated by a fix with ID
-      f_ID\[I\] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) :pre
-
-  {custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes
+{custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes :l
     possible attributes = id, mol, proc, procp1, type, element, mass,
                           x, y, z, xs, ys, zs, xu, yu, zu,
                           xsu, ysu, zsu, ix, iy, iz,
@@ -94,6 +83,15 @@ args = list of arguments for a particular style :l
       v_name = per-atom vector calculated by an atom-style variable with name
       d_name = per-atom floating point vector with name, managed by fix property/atom
       i_name = per-atom integer vector with name, managed by fix property/atom :pre
+
+{local} args = list of local attributes :l
+    possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\]
+      index = enumeration of local values
+      c_ID = local vector calculated by a compute with ID
+      c_ID\[I\] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
+      f_ID = local vector calculated by a fix with ID
+      f_ID\[I\] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) :pre
+
 :ule
 
 [Examples:]
@@ -225,7 +223,7 @@ This bounding box is convenient for many visualization programs.  The
 meaning of the 6 character flags for "xx yy zz" is the same as above.
 
 Note that the first two numbers on each line are now xlo_bound instead
-of xlo, etc, since they repesent a bounding box.  See "this
+of xlo, etc, since they represent a bounding box.  See "this
 section"_Section_howto.html#howto_12 of the doc pages for a geometric
 description of triclinic boxes, as defined by LAMMPS, simple formulas
 for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
@@ -331,10 +329,7 @@ bonds and colors.
 
 Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files
 can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a
-popular molecular viewing program.  See
-"Section 9"_Section_tools.html#vmd of the manual and the
-tools/lmp2vmd/README.txt file for more information about support in
-VMD for reading and visualizing LAMMPS dump files.
+popular molecular viewing program.
 
 :line
 
@@ -545,7 +540,7 @@ that the coordinate values may be far outside the box bounds printed
 with the snapshot.  Using {xsu}, {ysu}, {zsu} is similar to using
 {xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by
 the box size. Atoms that have passed through a periodic boundary will
-have the corresponding cooordinate increased or decreased by 1.0.
+have the corresponding coordinate increased or decreased by 1.0.
 
 The image flags can be printed directly using the {ix}, {iy}, {iz}
 attributes.  For periodic dimensions, they specify which image of the

doc/src/dump_custom_vtk.txt

@@ -1,339 +0,0 @@
- "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 custom/vtk command :h3
-
-[Syntax:]
-
-dump ID group-ID style N file args :pre
-
-ID = user-assigned name for the dump :ulb,l
-group-ID = ID of the group of atoms to be dumped :l
-style = {custom/vtk} :l
-N = dump every this many timesteps :l
-file = name of file to write dump info to :l
-args = list of arguments for a particular style :l
-  {custom/vtk} args = list of atom attributes
-    possible attributes = id, mol, proc, procp1, type, element, mass,
-                          x, y, z, xs, ys, zs, xu, yu, zu,
-                          xsu, ysu, zsu, ix, iy, iz,
-                          vx, vy, vz, fx, fy, fz,
-                          q, mux, muy, muz, mu,
-                          radius, diameter, omegax, omegay, omegaz,
-                          angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                          spin, eradius, ervel, erforce,
-                          c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
-
-      id = atom ID
-      mol = molecule ID
-      proc = ID of processor that owns atom
-      procp1 = ID+1 of processor that owns atom
-      type = atom type
-      element = name of atom element, as defined by "dump_modify"_dump_modify.html command
-      mass = atom mass
-      x,y,z = unscaled atom coordinates
-      xs,ys,zs = scaled atom coordinates
-      xu,yu,zu = unwrapped atom coordinates
-      xsu,ysu,zsu = scaled unwrapped atom coordinates
-      ix,iy,iz = box image that the atom is in
-      vx,vy,vz = atom velocities
-      fx,fy,fz = forces on atoms
-      q = atom charge
-      mux,muy,muz = orientation of dipole moment of atom
-      mu = magnitude of dipole moment of atom
-      radius,diameter = radius,diameter of spherical particle
-      omegax,omegay,omegaz = angular velocity of spherical particle
-      angmomx,angmomy,angmomz = angular momentum of aspherical particle
-      tqx,tqy,tqz = torque on finite-size particles
-      c_ID = per-atom vector calculated by a compute with ID
-      c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID
-      f_ID = per-atom vector calculated by a fix with ID
-      f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID
-      v_name = per-atom vector calculated by an atom-style variable with name :pre
-:ule
-
-[Examples:]
-
-dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
-dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke
-dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce :pre
-
-The style {custom/vtk} is similar to the "custom"_dump.html style but
-uses the VTK library to write data to VTK simple legacy or XML format
-depending on the filename extension specified. This can be either
-{*.vtk} for the legacy format or {*.vtp} and {*.vtu}, respectively,
-for the XML format; see the "VTK
-homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed
-description of these formats.  Since this naming convention conflicts
-with the way binary output is usually specified (see below),
-"dump_modify binary"_dump_modify.html allows to set the binary
-flag for this dump style explicitly.
-
-[Description:]
-
-Dump a snapshot of atom quantities to one or more files every N
-timesteps in a format readable by the "VTK visualization
-toolkit"_http://www.vtk.org or other visualization tools that use it,
-e.g. "ParaView"_http://www.paraview.org.  The timesteps on which dump
-output is written can also be controlled by a variable; see the
-"dump_modify every"_dump_modify.html command for details.
-
-Only information for atoms in the specified group is dumped.  The
-"dump_modify thresh and region"_dump_modify.html commands can also
-alter what atoms are included; see details below.
-
-As described below, special characters ("*", "%") in the filename
-determine the kind of output.
-
-IMPORTANT NOTE: Because periodic boundary conditions are enforced only
-on timesteps when neighbor lists are rebuilt, the coordinates of an
-atom written to a dump file may be slightly outside the simulation
-box.
-
-IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html
-option is invoked, the lines of atom information written to dump files
-will be in an indeterminate order for each snapshot.  This is even
-true when running on a single processor, if the "atom_modify
-sort"_atom_modify.html option is on, which it is by default.  In this
-case atoms are re-ordered periodically during a simulation, due to
-spatial sorting.  It is also true when running in parallel, because
-data for a single snapshot is collected from multiple processors, each
-of which owns a subset of the atoms.
-
-For the {custom/vtk} style, sorting is off by default. See the
-"dump_modify"_dump_modify.html doc page for details.
-
-:line
-
-The dimensions of the simulation box are written to a separate file
-for each snapshot (either in legacy VTK or XML format depending on
-the format of the main dump file) with the suffix {_boundingBox}
-appended to the given dump filename.
-
-For an orthogonal simulation box this information is saved as a
-rectilinear grid (legacy .vtk or .vtr XML format).
-
-Triclinic simulation boxes (non-orthogonal) are saved as
-hexahedrons in either legacy .vtk or .vtu XML format.
-
-Style {custom/vtk} allows you to specify a list of atom attributes
-to be written to the dump file for each atom.  Possible attributes
-are listed above.  In contrast to the {custom} style, the attributes
-are rearranged to ensure correct ordering of vector components
-(except for computes and fixes - these have to be given in the right
-order) and duplicate entries are removed.
-
-You cannot specify a quantity that is not defined for a particular
-simulation - such as {q} for atom style {bond}, since that atom style
-doesn't assign charges.  Dumps occur at the very end of a timestep,
-so atom attributes will include effects due to fixes that are applied
-during the timestep.  An explanation of the possible dump custom/vtk attributes
-is given below. Since position data is required to write VTK files "x y z"
-do not have to be specified explicitly.
-
-The VTK format uses a single snapshot of the system per file, thus
-a wildcard "*" must be included in the filename, as discussed below.
-Otherwise the dump files will get overwritten with the new snapshot
-each time.
-
-:line
-
-Dumps are performed on timesteps that are a multiple of N (including
-timestep 0) and on the last timestep of a minimization if the
-minimization converges.  Note that this means a dump will not be
-performed on the initial timestep after the dump command is invoked,
-if the current timestep is not a multiple of N.  This behavior can be
-changed via the "dump_modify first"_dump_modify.html command, which
-can also be useful if the dump command is invoked after a minimization
-ended on an arbitrary timestep.  N can be changed between runs by
-using the "dump_modify every"_dump_modify.html command.
-The "dump_modify every"_dump_modify.html command
-also allows a variable to be used to determine the sequence of
-timesteps on which dump files are written.  In this mode a dump on the
-first timestep of a run will also not be written unless the
-"dump_modify first"_dump_modify.html command is used.
-
-Dump filenames can contain two wildcard characters.  If a "*"
-character appears in the filename, then one file per snapshot is
-written and the "*" character is replaced with the timestep value.
-For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
-tmp.dump20000.vtk, etc.  Note that the "dump_modify pad"_dump_modify.html
-command can be used to insure all timestep numbers are the same length
-(e.g. 00010), which can make it easier to read a series of dump files
-in order with some post-processing tools.
-
-If a "%" character appears in the filename, then each of P processors
-writes a portion of the dump file, and the "%" character is replaced
-with the processor ID from 0 to P-1 preceded by an underscore character.
-For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ...
-tmp.dump_P-1.vtp, etc.  This creates smaller files and can be a fast
-mode of output on parallel machines that support parallel I/O for output.
-
-By default, P = the number of processors meaning one file per
-processor, but P can be set to a smaller value via the {nfile} or
-{fileper} keywords of the "dump_modify"_dump_modify.html command.
-These options can be the most efficient way of writing out dump files
-when running on large numbers of processors.
-
-For the legacy VTK format "%" is ignored and P = 1, i.e., only
-processor 0 does write files.
-
-Note that using the "*" and "%" characters together can produce a
-large number of small dump files!
-
-If {dump_modify binary} is used, the dump file (or files, if "*" or
-"%" is also used) is written in binary format.  A binary dump file
-will be about the same size as a text version, but will typically
-write out much faster.
-
-:line
-
-This section explains the atom attributes that can be specified as
-part of the {custom/vtk} style.
-
-The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx},
-{vy}, {vz}, {fx}, {fy}, {fz}, {q} attributes are self-explanatory.
-
-{id} is the atom ID.  {mol} is the molecule ID, included in the data
-file for molecular systems.  {type} is the atom type.  {element} is
-typically the chemical name of an element, which you must assign to
-each type via the "dump_modify element"_dump_modify.html command.
-More generally, it can be any string you wish to associate with an
-atom type.  {mass} is the atom mass.  {vx}, {vy}, {vz}, {fx}, {fy},
-{fz}, and {q} are components of atom velocity and force and atomic
-charge.
-
-There are several options for outputting atom coordinates.  The {x},
-{y}, {z} attributes are used to write atom coordinates "unscaled", in
-the appropriate distance "units"_units.html (Angstroms, sigma, etc).
-Additionaly, you can use {xs}, {ys}, {zs} if you want to also save the
-coordinates "scaled" to the box size, so that each value is 0.0 to
-1.0.  If the simulation box is triclinic (tilted), then all atom
-coords will still be between 0.0 and 1.0.  Use {xu}, {yu}, {zu} if you
-want the coordinates "unwrapped" by the image flags for each atom.
-Unwrapped means that if the atom has passed through a periodic
-boundary one or more times, the value is printed for what the
-coordinate would be if it had not been wrapped back into the periodic
-box.  Note that using {xu}, {yu}, {zu} means that the coordinate
-values may be far outside the box bounds printed with the snapshot.
-Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except
-that the unwrapped coordinates are scaled by the box size. Atoms that
-have passed through a periodic boundary will have the corresponding
-cooordinate increased or decreased by 1.0.
-
-The image flags can be printed directly using the {ix}, {iy}, {iz}
-attributes.  For periodic dimensions, they specify which image of the
-simulation box the atom is considered to be in.  An image of 0 means
-it is inside the box as defined.  A value of 2 means add 2 box lengths
-to get the true value.  A value of -1 means subtract 1 box length to
-get the true value.  LAMMPS updates these flags as atoms cross
-periodic boundaries during the simulation.
-
-The {mux}, {muy}, {muz} attributes are specific to dipolar systems
-defined with an atom style of {dipole}.  They give the orientation of
-the atom's point dipole moment.  The {mu} attribute gives the
-magnitude of the atom's dipole moment.
-
-The {radius} and {diameter} attributes are specific to spherical
-particles that have a finite size, such as those defined with an atom
-style of {sphere}.
-
-The {omegax}, {omegay}, and {omegaz} attributes are specific to
-finite-size spherical particles that have an angular velocity.  Only
-certain atom styles, such as {sphere} define this quantity.
-
-The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
-finite-size aspherical particles that have an angular momentum.  Only
-the {ellipsoid} atom style defines this quantity.
-
-The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that
-can sustain a rotational torque due to interactions with other
-particles.
-
-The {spin}, {eradius}, {ervel}, and {erforce} attributes are for
-particles that represent nuclei and electrons modeled with the
-electronic force field (EFF).  See "atom_style
-electron"_atom_style.html and "pair_style eff"_pair_eff.html for more
-details.
-
-The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays
-calculated by a "compute"_compute.html to be output.  The ID in the
-attribute should be replaced by the actual ID of the compute that has
-been defined previously in the input script.  See the
-"compute"_compute.html command for details.  There are computes for
-calculating the per-atom energy, stress, centro-symmetry parameter,
-and coordination number of individual atoms.
-
-Note that computes which calculate global or local quantities, as
-opposed to per-atom quantities, cannot be output in a dump custom/vtk
-command.  Instead, global quantities can be output by the
-"thermo_style custom"_thermo_style.html command, and local quantities
-can be output by the dump local command.
-
-If {c_ID} is used as an attribute, then the per-atom vector calculated
-by the compute is printed.  If {c_ID\[N\]} is used, then N must be in
-the range from 1-M, which will print the Nth column of the M-length
-per-atom array calculated by the compute.
-
-The {f_ID} and {f_ID\[N\]} attributes allow vector or array per-atom
-quantities calculated by a "fix"_fix.html to be output.  The ID in the
-attribute should be replaced by the actual ID of the fix that has been
-defined previously in the input script.  The "fix
-ave/atom"_fix_ave_atom.html command is one that calculates per-atom
-quantities.  Since it can time-average per-atom quantities produced by
-any "compute"_compute.html, "fix"_fix.html, or atom-style
-"variable"_variable.html, this allows those time-averaged results to
-be written to a dump file.
-
-If {f_ID} is used as a attribute, then the per-atom vector calculated
-by the fix is printed.  If {f_ID\[N\]} is used, then N must be in the
-range from 1-M, which will print the Nth column of the M-length
-per-atom array calculated by the fix.
-
-The {v_name} attribute allows per-atom vectors calculated by a
-"variable"_variable.html to be output.  The name in the attribute
-should be replaced by the actual name of the variable that has been
-defined previously in the input script.  Only an atom-style variable
-can be referenced, since it is the only style that generates per-atom
-values.  Variables of style {atom} can reference individual atom
-attributes, per-atom atom attributes, thermodynamic keywords, or
-invoke other computes, fixes, or variables when they are evaluated, so
-this is a very general means of creating quantities to output to a
-dump file.
-
-See "Section 10"_Section_modify.html of the manual for information
-on how to add new compute and fix styles to LAMMPS to calculate
-per-atom quantities which could then be output into dump files.
-
-:line
-
-[Restrictions:]
-
-The {custom/vtk} style does not support writing of gzipped dump files.
-
-The {custom/vtk} dump style is part of the USER-VTK 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.
-
-To use this dump style, you also must link to the VTK library.  See
-the info in lib/vtk/README and insure the Makefile.lammps file in that
-directory is appropriate for your machine.
-
-The {custom/vtk} dump style neither supports buffering nor custom
-format strings.
-
-[Related commands:]
-
-"dump"_dump.html, "dump image"_dump_image.html,
-"dump_modify"_dump_modify.html, "undump"_undump.html
-
-[Default:]
-
-By default, files are written in ASCII format. If the file extension
-is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.
-

doc/src/dump_h5md.txt

@@ -17,9 +17,7 @@ group-ID = ID of the group of atoms to be imaged :l
 h5md = 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.h5 = name of file to write to :l
-args = list of data elements to dump, with their dump "subintervals".
-At least one element must be given and image may only be present if
-position is specified first. :l
+args = list of data elements to dump, with their dump "subintervals"
   position options
   image
   velocity options
@@ -29,15 +27,17 @@ position is specified first. :l
   box value = {yes} or {no}
   create_group value = {yes} or {no}
   author value = quoted string :pre
+:ule
 
-For the elements {position}, {velocity}, {force} and {species}, one
-may specify a sub-interval to write the data only every N_element
+Note that at least one element must be specified and image may only be
+present if position is specified first.
+
+For the elements {position}, {velocity}, {force} and {species}, a
+sub-interval may be specified to write the data only every N_element
 iterations of the dump (i.e. every N*N_element time steps). This is
-specified by the option
+specified by this option directly following the element declaration:
 
-  every N_element :pre
-
-that follows directly the element declaration.
+every N_element :pre
 
 :ule
 

doc/src/dump_image.txt

@@ -99,7 +99,7 @@ included in the image or movie and how it appears.  A series of such
 images can easily be manually converted into an animated movie of your
 simulation or the process can be automated without writing the
 intermediate files using the dump movie style; see further details
-below.  Other dump styles store snapshots of numerical data asociated
+below.  Other dump styles store snapshots of numerical data associated
 with atoms in various formats, as discussed on the "dump"_dump.html
 doc page.
 
@@ -237,7 +237,7 @@ diameter, which can be used as the {diameter} setting.
 
 :line
 
-The various kewords listed above control how the image is rendered.
+The various keywords listed above control how the image is rendered.
 As listed below, all of the keywords have defaults, most of which you
 will likely not need to change.  The "dump modify"_dump_modify.html
 also has options specific to the dump image style, particularly for
@@ -261,7 +261,7 @@ the input script defines, e.g. Angstroms.
 The {bond} keyword allows to you to alter how bonds are drawn.  A bond
 is only drawn if both atoms in the bond are being drawn due to being
 in the specified group and due to other selection criteria
-(e.g. region, threshhold settings of the
+(e.g. region, threshold settings of the
 "dump_modify"_dump_modify.html command).  By default, bonds are drawn
 if they are defined in the input data file as read by the
 "read_data"_read_data.html command.  Using {none} for both the bond
@@ -356,7 +356,7 @@ is used to define body particles with internal state
 body style.  If this keyword is not used, such particles will be drawn
 as spheres, the same as if they were regular atoms.
 
-The "body"_body.html doc page descibes the body styles LAMMPS
+The "body"_body.html doc page describes the body styles LAMMPS
 currently supports, and provides more details as to the kind of body
 particles they represent and how they are drawn by this dump image
 command.  For all the body styles, individual atoms can be either a
@@ -442,7 +442,7 @@ degrees.
 
 The {center} keyword determines the point in simulation space that
 will be at the center of the image.  {Cx}, {Cy}, and {Cz} are
-speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
+specified as fractions of the box dimensions, so that (0.5,0.5,0.5) is
 the center of the simulation box.  These values do not have to be
 between 0.0 and 1.0, if you want the simulation box to be offset from
 the center of the image.  Note, however, that if you choose strange
@@ -476,8 +476,8 @@ smaller.  {Zfactor} must be a value > 0.0.
 The {persp} keyword determines how much depth perspective is present
 in the image.  Depth perspective makes lines that are parallel in
 simulation space appear non-parallel in the image.  A {pfactor} value
-of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
-which is an orthographic rendering with no persepctive.  A {pfactor}
+of 0.0 means that parallel lines will meet at infinity (1.0/pfactor),
+which is an orthographic rendering with no perspective.  A {pfactor}
 value between 0.0 and 1.0 will introduce more perspective.  A {pfactor}
 value > 1 will create a highly skewed image with a large amount of
 perspective.
@@ -638,7 +638,7 @@ pipe:: Input/output error :pre
 which can be safely ignored. Other warnings
 and errors have to be addressed according to the FFmpeg documentation.
 One known issue is that certain movie file formats (e.g. MPEG level 1
-and 2 format streams) have video bandwith limits that can be crossed
+and 2 format streams) have video bandwidth limits that can be crossed
 when rendering too large of image sizes. Typical warnings look like
 this:
 

doc/src/dump_modify.txt

@@ -426,7 +426,7 @@ regions.
 
 The {scale} keyword applies only to the dump {atom} style.  A scale
 value of {yes} means atom coords are written in normalized units from
-0.0 to 1.0 in each box dimension.  If the simluation box is triclinic
+0.0 to 1.0 in each box dimension.  If the simulation box is triclinic
 (tilted), then all atom coords will still be between 0.0 and 1.0.  A
 value of {no} means they are written in absolute distance units
 (e.g. Angstroms or sigma).
@@ -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 operator.  Boolean values can
+which may be useful for the comparison 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.

doc/src/dump_molfile.txt

@@ -34,10 +34,7 @@ to one or more files every N timesteps in one of several formats.
 Only information for atoms in the specified group is dumped.  This
 specific dump style uses molfile plugins that are bundled with the
 "VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
-analysis program.  See "Section 9"_Section_tools.html#vmd of the
-manual and the tools/lmp2vmd/README.txt file for more information
-about support in VMD for reading and visualizing native LAMMPS dump
-files.
+analysis program.
 
 Unless the filename contains a * character, the output will be written
 to one single file with the specified format. Otherwise there will be