patch 17Mar17

Remove unneeded restart_peratom flags in USER-DPD package

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 +1,6 @@
 /html
+/spelling
+/LAMMPS.epub
+/LAMMPS.mobi
+/Manual.pdf
+/Developer.pdf

doc/Makefile

@@ -22,7 +22,7 @@ endif
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean html pdf old venv
+.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
 
 # ------------------------------------------
 
@@ -32,9 +32,11 @@ help:
 	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
 	@echo "  old        create old-style HTML doc pages in old dir"
 	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
+	@echo "  epub       create ePUB format manual for e-book readers"
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
+	@echo "  anchor_check  scan for duplicate anchor labels"
 
 # ------------------------------------------
 
@@ -42,13 +44,20 @@ clean-all:
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
 
 clean:
-	rm -rf $(RSTDIR)
+	rm -rf $(RSTDIR) html
+	rm -rf spelling
+
+clean-spelling:
+	rm -rf spelling
 
 html: $(OBJECTS)
 	@(\
 		. $(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
@@ -63,6 +72,31 @@ 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
+	@cp src/JPG/lammps-logo.png epub/
+	@(\
+		. $(VENV)/bin/activate ;\
+		cp -r src/* $(RSTDIR)/ ;\
+		sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		deactivate ;\
+	)
+	@mv  epub/LAMMPS.epub .
+	@rm -rf epub
+	@echo "Build finished. The ePUB manual file is created."
+
 pdf: utils/txt2html/txt2html.exe
 	@(\
 		cd src; \
@@ -97,6 +131,13 @@ fetch:
 
 txt2html: utils/txt2html/txt2html.exe
 
+anchor_check : $(TXT2RST)
+	@(\
+		. $(VENV)/bin/activate ;\
+		doc_anchor_check src/*.txt ;\
+		deactivate ;\
+	)
+
 # ------------------------------------------
 
 utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp

doc/README

@@ -1,13 +1,14 @@
 LAMMPS Documentation
 
 Depending on how you obtained LAMMPS, this directory has 2 or 3
-sub-directories and optionally 2 PDF files:
+sub-directories and optionally 2 PDF files and an ePUB file:
 
 src             content files for LAMMPS documentation
 html            HTML version of the LAMMPS manual (see html/Manual.html)
 tools           tools and settings for building the documentation
 Manual.pdf      large PDF version of entire manual
 Developer.pdf   small PDF with info about how LAMMPS is structured
+LAMMPS.epub     Manual in ePUB format
 
 If you downloaded LAMMPS as a tarball from the web site, all these
 directories and files should be included.
@@ -49,6 +50,7 @@ make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
 make old          # generate old-style HTML pages in old dir via txt2html
 make fetch        # fetch HTML doc pages and 2 PDF files from web site
                   #   as a tarball and unpack into html dir and 2 PDFs
+make epub         # generate LAMMPS.epub in ePUB format using Sphinx 
 make clean        # remove intermediate RST files created by HTML build
 make clean-all    # remove entire build folder and any cached data
 
@@ -91,3 +93,23 @@ This will install virtualenv from the Python Package Index.
 ----------------
 
 Installing prerequisites for PDF build
+
+[TBA]
+
+----------------
+
+Installing prerequisites for epub build
+
+## ePUB
+
+Same as for HTML. This uses the same tools and configuration
+files as the HTML tree.
+
+For converting the generated ePUB file to a mobi format file
+(for e-book readers like Kindle, that cannot read ePUB), you
+also need to have the 'ebook-convert' tool from the "calibre"
+software installed. http://calibre-ebook.com/
+You first create the ePUB file with 'make epub' and then do:
+
+ebook-convert LAMMPS.epub LAMMPS.mobi
+

doc/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/bond_oxdna_fene.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+$$ 
+  E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
+$$
+
+\end{document}

doc/src/Eqs/fix_grem.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  T_{eff} = \lambda + \eta (H - H_0)
+$$
+
+\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_tersoff_mod_c.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+\begin{eqnarray*}
+  V_{ij}  & =  & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pressure.tex

@@ -3,7 +3,7 @@
 \begin{document}
 
 $$
-   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N} r_i \bullet f_i}{dV}
+   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N'} r_i \bullet f_i}{dV}
 $$
 
 \end{document}

doc/src/Eqs/pressure_tensor.tex

@@ -4,7 +4,7 @@
 
 $$
    P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} + 
-   \frac{\sum_{k}^{N} r_{k_I} f_{k_J}}{V}
+   \frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V}
 $$
 
 \end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="18 Oct 2016 version">
+<META NAME="docnumber" CONTENT="17 Mar 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
-18 Oct 2016 version :c,h4
+17 Mar 2017 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -106,7 +106,7 @@ the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
 "x".
 
 How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable doc page for details.
+of variable it is; see the "variable"_variable.html doc page for details.
 It can be a variable that stores multiple text strings, and return one
 of them.  The returned text string can be multiple "words" (space
 separated) which will then be interpreted as multiple arguments in the
@@ -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,
@@ -528,8 +528,11 @@ These are additional commands in USER packages, which can be used if
 package"_Section_start.html#start_3.
 
 "dump custom/vtk"_dump_custom_vtk.html,
+"dump nc"_dump_nc.html,
+"dump nc/mpiio"_dump_nc.html,
 "group2ndx"_group2ndx.html,
-"ndx2group"_group2ndx.html :tb(c=3,ea=c)
+"ndx2group"_group2ndx.html,
+"temper/grem"_temper_grem.html :tb(c=3,ea=c)
 
 :line
 
@@ -578,8 +581,9 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "indent"_fix_indent.html,
 "langevin (k)"_fix_langevin.html,
 "lineforce"_fix_lineforce.html,
-"momentum"_fix_momentum.html,
+"momentum (k)"_fix_momentum.html,
 "move"_fix_move.html,
+"mscg"_fix_mscg.html,
 "msst"_fix_msst.html,
 "neb"_fix_neb.html,
 "nph (ko)"_fix_nh.html,
@@ -630,10 +634,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
+"rigid/small/nph (o)"_fix_rigid.html,
+"rigid/small/npt (o)"_fix_rigid.html,
+"rigid/small/nve (o)"_fix_rigid.html,
+"rigid/small/nvt (o)"_fix_rigid.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "spring"_fix_spring.html,
@@ -683,8 +687,10 @@ 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,
 "imd"_fix_imd.html,
 "ipi"_fix_ipi.html,
 "langevin/drude"_fix_langevin_drude.html,
@@ -697,7 +703,10 @@ package"_Section_start.html#start_3.
 "meso"_fix_meso.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
+"nve/dot"_fix_nve_dot.html,
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
+"nvk"_fix_nvk.html,
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
 "nph/eff"_fix_nh_eff.html,
 "npt/eff"_fix_nh_eff.html,
@@ -763,6 +772,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "erotate/sphere"_compute_erotate_sphere.html,
 "erotate/sphere/atom"_compute_erotate_sphere_atom.html,
 "event/displace"_compute_event_displace.html,
+"global/atom"_compute_global_atom.html,
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
 "gyration/chunk"_compute_gyration_chunk.html,
@@ -884,6 +894,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "body"_pair_body.html,
 "bop"_pair_bop.html,
 "born (go)"_pair_born.html,
+"born/coul/dsf"_pair_born.html,
+"born/coul/dsf/cs"_pair_born.html,
 "born/coul/long (go)"_pair_born.html,
 "born/coul/long/cs"_pair_born.html,
 "born/coul/msm (o)"_pair_born.html,
@@ -907,10 +919,10 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (o)"_pair_dpd.html,
-"dpd/tstat (o)"_pair_dpd.html,
+"dpd (go)"_pair_dpd.html,
+"dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
-"eam (gkot)"_pair_eam.html,
+"eam (gkiot)"_pair_eam.html,
 "eam/alloy (gkot)"_pair_eam.html,
 "eam/fs (gkot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
@@ -958,7 +970,7 @@ 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,
@@ -977,11 +989,12 @@ KOKKOS, o = USER-OMP, t = OPT.
 "table (gko)"_pair_table.html,
 "tersoff (gkio)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/mod/c (o)"_pair_tersoff_mod.html,
 "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
 "tri/lj"_pair_tri_lj.html,
-"vashishta (o)"_pair_vashishta.html,
+"vashishta (ko)"_pair_vashishta.html,
 "vashishta/table (o)"_pair_vashishta.html,
 "yukawa (go)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
@@ -991,6 +1004,7 @@ These are additional pair styles in USER packages, which can be used
 if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.
 
+"agni (o)"_pair_agni.html,
 "awpmd/cut"_pair_awpmd.html,
 "buck/mdf"_pair_mdf.html,
 "coul/cut/soft (o)"_pair_lj_soft.html,
@@ -1003,6 +1017,7 @@ 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,
@@ -1024,6 +1039,11 @@ package"_Section_start.html#start_3.
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx"_pair_multi_lucy_rx.html,
+"oxdna/coaxstk"_pair_oxdna.html,
+"oxdna/excv"_pair_oxdna.html,
+"oxdna/hbond"_pair_oxdna.html,
+"oxdna/stk"_pair_oxdna.html,
+"oxdna/xstk"_pair_oxdna.html,
 "quip"_pair_quip.html,
 "reax/c (k)"_pair_reax_c.html,
 "smd/hertz"_pair_smd_hertz.html,
@@ -1058,7 +1078,7 @@ 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,
@@ -1072,7 +1092,8 @@ if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.
 
 "harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
+"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"oxdna/fene"_bond_oxdna.html :tb(c=4,ea=c)
 
 :line
 
@@ -1090,7 +1111,7 @@ 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,
@@ -1126,7 +1147,7 @@ USER-OMP, t = OPT.
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
 "charmm (ko)"_dihedral_charmm.html,
-"class2 (o)"_dihedral_class2.html,
+"class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
 "helix (o)"_dihedral_helix.html,
 "multi/harmonic (o)"_dihedral_multi_harmonic.html,
@@ -1158,7 +1179,7 @@ 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
@@ -55,12 +55,13 @@ LAMMPS errors are detected at setup time; others like a bond
 stretching too far may not occur until the middle of a run.
 
 LAMMPS tries to flag errors and print informative error messages so
-you can fix the problem.  Of course, LAMMPS cannot figure out your
-physics or numerical mistakes, like choosing too big a timestep,
-specifying erroneous force field coefficients, or putting 2 atoms on
-top of each other!  If you run into errors that LAMMPS doesn't catch
-that you think it should flag, please send an email to the
-"developers"_http://lammps.sandia.gov/authors.html.
+you can fix the problem.  For most errors it will also print the last
+input script command that it was processing.  Of course, LAMMPS cannot
+figure out your physics or numerical mistakes, like choosing too big a
+timestep, specifying erroneous force field coefficients, or putting 2
+atoms on top of each other!  If you run into errors that LAMMPS
+doesn't catch that you think it should flag, please send an email to
+the "developers"_http://lammps.sandia.gov/authors.html.
 
 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by
@@ -79,12 +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
@@ -561,11 +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
 
@@ -899,7 +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
@@ -979,7 +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
 
@@ -1314,7 +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
@@ -1992,7 +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
 
@@ -2075,7 +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
 
@@ -2118,7 +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
 
@@ -2278,7 +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
 
@@ -2628,11 +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
 
@@ -2693,15 +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
 
@@ -2722,11 +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
 
@@ -2734,7 +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
 
@@ -2747,7 +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
 
@@ -2777,7 +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
 
@@ -2822,7 +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
 
@@ -2868,11 +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
 
@@ -2922,7 +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
 
@@ -3066,7 +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
 
@@ -3511,12 +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
@@ -3625,7 +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
 
@@ -4372,7 +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
 
@@ -4604,11 +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
 
@@ -4957,7 +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
 
@@ -6158,7 +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
 
@@ -6186,7 +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
@@ -6450,15 +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
 
@@ -6724,7 +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
 
@@ -6738,7 +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
 
@@ -7300,7 +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
 
@@ -7348,7 +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
@@ -7513,7 +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
 
@@ -7539,7 +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
@@ -7779,7 +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
@@ -8029,7 +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
 
@@ -8116,11 +8129,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd
 
 {Out of range atoms - cannot compute PPPM} :dt
 
@@ -8132,11 +8145,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd
 
 {Out of range atoms - cannot compute PPPMDisp} :dt
 
@@ -8148,11 +8161,11 @@ boundary of a processor's sub-domain has moved more than 1/2 the
 rebuilt and atoms being migrated to new processors.  This also means
 you may be missing pairwise interactions that need to be computed.
 The solution is to change the re-neighboring criteria via the
-"neigh_modify"_neigh_modify command.  The safest settings are "delay 0
-every 1 check yes".  Second, it may mean that an atom has moved far
-outside a processor's sub-domain or even the entire simulation box.
-This indicates bad physics, e.g. due to highly overlapping atoms, too
-large a timestep, etc. :dd
+"neigh_modify"_neigh_modify.html command.  The safest settings are
+"delay 0 every 1 check yes".  Second, it may mean that an atom has
+moved far outside a processor's sub-domain or even the entire
+simulation box. This indicates bad physics, e.g. due to highly
+overlapping atoms, too large a timestep, etc. :dd
 
 {Overflow of allocated fix vector storage} :dt
 
@@ -8650,7 +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
 
@@ -8935,11 +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
 
@@ -9153,7 +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
 
@@ -10012,7 +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
@@ -10074,7 +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
@@ -10142,7 +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
 
@@ -10641,7 +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
 
@@ -10653,7 +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
 
@@ -10694,7 +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
@@ -10783,7 +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
 
@@ -11070,7 +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
 
@@ -11401,7 +11414,7 @@ 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
@@ -11439,7 +11452,7 @@ 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
@@ -11524,7 +11537,7 @@ 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
 
@@ -11576,7 +11589,7 @@ 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
@@ -11873,7 +11886,7 @@ 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_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

@@ -573,7 +573,7 @@ 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 +618,7 @@ 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
@@ -863,7 +863,7 @@ 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 +982,10 @@ 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 +1032,10 @@ 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 +1396,7 @@ 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 +1529,7 @@ 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 +1589,7 @@ 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 +1644,14 @@ 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
@@ -1854,13 +1858,19 @@ internal LAMMPS operations.  Note that LAMMPS classes are defined
 within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
 application.
 
-Library.cpp contains these 5 basic functions:
+Library.cpp contains these functions for creating and destroying an
+instance of LAMMPS and sending it commands to execute.  See the
+documentation in the src/library.cpp file for details:
 
 void lammps_open(int, char **, MPI_Comm, void **)
+void lammps_open_no_mpi(int, char **, void **)
 void lammps_close(void *)
 int lammps_version(void *)
 void lammps_file(void *, char *)
-char *lammps_command(void *, char *) :pre
+char *lammps_command(void *, char *)
+void lammps_commands_list(void *, int, char **)
+void lammps_commands_string(void *, char *)
+void lammps_free(void *) :pre
 
 The lammps_open() function is used to initialize LAMMPS, passing in a
 list of strings as if they were "command-line
@@ -1880,6 +1890,10 @@ half to the other code and run both codes simultaneously before
 syncing them up periodically.  Or it might instantiate multiple
 instances of LAMMPS to perform different calculations.
 
+The lammps_open_no_mpi() function is similar except that no MPI
+communicator is passed from the caller.  Instead, MPI_COMM_WORLD is
+used to instantiate LAMMPS, and MPI is initialized if necessary.
+
 The lammps_close() function is used to shut down an instance of LAMMPS
 and free all its memory.
 
@@ -1891,44 +1905,106 @@ changes to the LAMMPS command syntax between versions. The returned
 LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
 20150902) that grows with every new LAMMPS version.
 
-The lammps_file() and lammps_command() functions are used to pass a
-file or string to LAMMPS as if it were an input script or single
-command in an input script.  Thus the calling code can read or
-generate a series of LAMMPS commands one line at a time and pass it
-thru the library interface to setup a problem and then run it,
-interleaving the lammps_command() calls with other calls to extract
-information from LAMMPS, perform its own operations, or call another
-code's library.
+The lammps_file(), lammps_command(), lammps_commands_list(), and
+lammps_commands_string() functions are used to pass one or more
+commands to LAMMPS to execute, the same as if they were coming from an
+input script.
 
-Other useful functions are also included in library.cpp.  For example:
+Via these functions, the calling code can read or generate a series of
+LAMMPS commands one or multiple at a time and pass it thru the library
+interface to setup a problem and then run it in stages.  The caller
+can interleave the command function calls with operations it performs,
+calls to extract information from or set information within LAMMPS, or
+calls to another code's library.
+
+The lammps_file() function passes the filename of an input script.
+The lammps_command() function passes a single command as a string.
+The lammps_commands_list() function passes multiple commands in a
+char** list.  In both lammps_command() and lammps_commands_list(),
+individual commands may or may not have a trailing newline.  The
+lammps_commands_string() function passes multiple commands
+concatenated into one long string, separated by newline characters.
+In both lammps_commands_list() and lammps_commands_string(), a single
+command can be spread across multiple lines, if the last printable
+character of all but the last line is "&", the same as if the lines
+appeared in an input script.
+
+The lammps_free() function is a clean-up function to free memory that
+the library allocated previously via other function calls.  See
+comments in src/library.cpp file for which other functions need this
+clean-up.
+
+Library.cpp also contains these functions for extracting information
+from LAMMPS and setting value within LAMMPS.  Again, see the
+documentation in the src/library.cpp file for details, including
+which quantities can be queried by name:
 
 void *lammps_extract_global(void *, char *)
+void lammps_extract_box(void *, double *, double *, 
+                        double *, double *, double *, int *, int *)
 void *lammps_extract_atom(void *, char *)
 void *lammps_extract_compute(void *, char *, int, int)
 void *lammps_extract_fix(void *, char *, int, int, int, int)
-void *lammps_extract_variable(void *, char *, char *)
-int lammps_set_variable(void *, char *, char *)
+void *lammps_extract_variable(void *, char *, char *) :pre
+
+void lammps_reset_box(void *, double *, double *, double, double, double)
+int lammps_set_variable(void *, char *, char *) :pre
+
+double lammps_get_thermo(void *, char *)
 int lammps_get_natoms(void *)
-void lammps_get_coords(void *, double *)
-void lammps_put_coords(void *, double *) :pre
+void lammps_gather_atoms(void *, double *)
+void lammps_scatter_atoms(void *, double *) :pre
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
+                         imageint *, int) :pre
 
-These can extract various global or per-atom quantities from LAMMPS as
-well as values calculated by a compute, fix, or variable.  The
-"set_variable" function can set an existing string-style variable to a
-new value, so that subsequent LAMMPS commands can access the variable.
-The "get" and "put" operations can retrieve and reset atom
-coordinates.  See the library.cpp file and its associated header file
-library.h for details.
+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 key idea of the library interface is that you can write any
-functions you wish to define how your code talks to LAMMPS and add
-them to src/library.cpp and src/library.h, as well as to the "Python
-interface"_Section_python.html.  The routines you add can access or
-change any LAMMPS data you wish.  The examples/COUPLE and python
-directories have example C++ and C and Python codes which show how a
-driver code can link to LAMMPS as a library, run LAMMPS on a subset of
-processors, grab data from LAMMPS, change it, and put it back into
-LAMMPS.
+The lammps_reset_box() function resets the size and shape of the
+simulation box, e.g. as part of restoring a previously extracted and
+saved state of a simulation.
+
+The lammps_set_variable() function can set an existing string-style
+variable to a new string value, so that subsequent LAMMPS commands can
+access the variable.
+
+The lammps_get_thermo() function returns the current value of a thermo
+keyword as a double 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 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 kinds of values, 
+passed by the caller, to each atom owned by individual processors.
+
+The lammps_create_atoms() function takes a list of N atoms as input
+with atom types and coords (required), an optionally atom IDs and
+velocities and image flags.  It uses the coords of each atom to assign
+it as a new atom to the processor that owns it.  This function is
+useful to add atoms to a simulation or (in tandem with
+lammps_reset_box()) to restore a previously extracted and saved state
+of a simulation.  Additional properties for the new atoms can then be
+assigned via the lammps_scatter_atoms() or lammps_extract_atom()
+functions.
+
+The examples/COUPLE and python directories have example C++ and C and
+Python codes which show how a driver code can link to LAMMPS as a
+library, run LAMMPS on a subset of processors, grab data from LAMMPS,
+change it, and put it back into LAMMPS.
+
+NOTE: You can write code for additional functions as needed to define
+how your code talks to LAMMPS and add them to src/library.cpp and
+src/library.h, as well as to the "Python
+interface"_Section_python.html.  The added functions can access or
+change any LAMMPS data you wish.
 
 :line
 
@@ -1941,7 +2017,7 @@ 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
 
@@ -2027,7 +2103,7 @@ 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.
@@ -2053,7 +2129,7 @@ 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
@@ -2196,7 +2272,7 @@ 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.
@@ -2281,7 +2357,7 @@ 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:
@@ -2352,7 +2428,7 @@ 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
@@ -2372,7 +2448,7 @@ 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).
@@ -2406,7 +2482,7 @@ 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
@@ -2425,7 +2501,7 @@ 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
@@ -2479,7 +2555,7 @@ 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
@@ -2501,7 +2577,7 @@ 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
@@ -2595,13 +2671,16 @@ 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
@@ -2632,45 +2711,55 @@ 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).
-
-The mentioned energy transfer will typically lead to a a small drift
+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
 temp/chunk"_compute_temp_chunk.html commands.  The internal kinetic
@@ -2689,14 +2778,20 @@ 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:
 
@@ -2717,7 +2812,7 @@ 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):
@@ -2771,7 +2866,7 @@ temp/drude"_compute_temp_drude.html. This requires also to use the
 command {comm_modify vel yes}.
 
 Short-range damping of the induced dipole interactions can be achieved
-using Thole functions through the the "pair style
+using Thole functions through the "pair style
 thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
 with a Coulomb pair style. It may be useful to use {coul/long/cs} or
 similar from the CORESHELL package if the core and Drude particle come
@@ -2818,9 +2913,13 @@ Phys, 79, 926 (1983).
 :link(Shinoda)
 [(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

@@ -366,11 +366,11 @@ complementary modeling tasks.
 "DL_POLY"_dlpoly
 "Tinker"_tinker :ul
 
-:link(charmm,http://www.scripps.edu/brooks)
-:link(amber,http://amber.scripps.edu)
+:link(charmm,http://www.charmm.org)
+:link(amber,http://ambermd.org)
 :link(namd,http://www.ks.uiuc.edu/Research/namd/)
 :link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
-:link(dlpoly,http://www.cse.clrc.ac.uk/msi/software/DL_POLY)
+:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC)
 :link(tinker,http://dasher.wustl.edu/tinker)
 
 CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for

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_packages.txt

@@ -84,7 +84,7 @@ Package, Description, Author(s), Doc page, Example, Library
 "PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
 "POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
 "PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
-"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax
+"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
 "REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
 "RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
 "SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
@@ -94,7 +94,7 @@ Package, Description, Author(s), Doc page, Example, Library
 :tb(ea=c)
 
 The "Authors" column lists a name(s) if a specific person is
-responible for creating and maintaining the package.
+responsible for creating and maintaining the package.
 
 (1) The COLLOID package includes Fast Lubrication Dynamics pair styles
 which were created by Amit Kumar and Michael Bybee from Jonathan
@@ -462,7 +462,7 @@ options you are optimizing for: CPU acceleration via OpenMP, GPU
 acceleration, or Intel Xeon Phi.  (You can build multiple times to
 create LAMMPS executables for different hardware.)  It also requires a
 C++11 compatible compiler.  For GPUs, the NVIDIA "nvcc" compiler is
-used, and an appopriate KOKKOS_ARCH setting should be made in your
+used, and an appropriate KOKKOS_ARCH setting should be made in your
 Makefile.machine for your GPU hardware and NVIDIA software.
 
 The simplest way to do this is to use Makefile.kokkos_cuda or
@@ -955,8 +955,8 @@ multi-replica simulations in LAMMPS.  Multi-replica methods included
 in the package are nudged elastic band (NEB), parallel replica
 dynamics (PRD), temperature accelerated dynamics (TAD), parallel
 tempering, and a verlet/split algorithm for performing long-range
-Coulombics on one set of processors, and the remainded of the force
-field calcalation on another set.
+Coulombics on one set of processors, and the remainder of the force
+field calculation on another set.
 
 To install via make or Make.py:
 
@@ -1140,6 +1140,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
 "USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
 "USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
+"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Edinburgh), src/USER-CGDNA/README, USER/cgdna, -, -
 "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
 "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
 "USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
@@ -1153,6 +1154,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
 "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@@ -1174,7 +1176,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 :link(VMD,http://www.ks.uiuc.edu/Research/vmd)
 
 The "Authors" column lists a name(s) if a specific person is
-responible for creating and maintaining the package.
+responsible for creating and maintaining the package.
 
 (1) The ATC package was created by Reese Jones, Jeremy Templeton, and
 Jon Zimmerman (Sandia).
@@ -1283,6 +1285,31 @@ him directly if you have questions.
 
 :line
 
+USER-CGDNA package :link(USER-CGDNA),h5
+
+Contents: The CGDNA package implements coarse-grained force fields for
+single- and double-stranded DNA. This is at the moment mainly the
+oxDNA model, developed by Doye, Louis and Ouldridge at the University
+of Oxford.  The package also contains Langevin-type rigid-body
+integrators with improved stability.
+
+See these doc pages to get started:
+
+"bond_style oxdna/fene"_bond_oxdna.html
+"pair_style oxdna/..."_pair_oxdna.html
+"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
+
+Supporting info: /src/USER-CGDNA/README, "bond_style
+oxdna/fene"_bond_oxdna.html, "pair_style
+oxdna/..."_pair_oxdna.html, "fix
+nve/dotc/langevin"_fix_nve_dotc_langevin.html
+
+Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
+at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk).  Contact him directly if
+you have any questions.
+
+:line
+
 USER-COLVARS package :link(USER-COLVARS),h5
 
 Contents: COLVARS stands for collective variables which can be used to
@@ -1598,6 +1625,30 @@ The person who created this package is Axel Kohlmeyer at Temple U
 
 :line
 
+USER-NC-DUMP package :link(USER-NC-DUMP),h5
+
+Contents: Dump styles for writing NetCDF format files.  NetCDF is a binary,
+portable, self-describing file format on top of HDF5. The file format
+contents follow the AMBER NetCDF trajectory conventions
+(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions to this
+convention. This package implements a "dump nc"_dump_nc.html command
+and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
+in this format.  See src/USER-NC-DUMP/README for more details.
+
+NetCDF files can be directly visualized with the following tools:
+
+Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
+and all of the above extensions. :ulb,l
+VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
+AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
+a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+
+The person who created these files is Lars Pastewka at
+Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
+Contact him directly if you have questions.
+
+:line
+
 USER-OMP package :link(USER-OMP),h5
 
 Supporting info:
@@ -1727,7 +1778,7 @@ particularly with respect to the charge equilibration calculation.  It
 should also be easier to build and use since there are no complicating
 issues with Fortran memory allocation or linking to a Fortran library.
 
-For technical details about this implemention of ReaxFF, see
+For technical details about this implementation of ReaxFF, see
 this paper:
 
 Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
@@ -1797,7 +1848,7 @@ See this doc page to get started:
 
 The persons who created the USER-SMTBQ package are Nicolas Salles,
 Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
-these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr.  Contact
+these email addresses: lammps@u-bourgogne.fr, nsalles@laas.fr.  Contact
 them directly if you have any questions.
 
 Examples: examples/USER/smtbq

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

@@ -8,19 +8,26 @@
 
 11. Python interface to LAMMPS :h3
 
-LAMMPS can work together with Python in two ways.  First, Python can
+LAMMPS can work together with Python in three ways.  First, Python can
 wrap LAMMPS through the "LAMMPS library
 interface"_Section_howto.html#howto_19, so that a Python script can
 create one or more instances of LAMMPS and launch one or more
 simulations.  In Python lingo, this is "extending" Python with LAMMPS.
 
-Second, LAMMPS can use the Python interpreter, so that a LAMMPS input
+Second, the low-level Python interface can be used indirectly through the
+PyLammps and IPyLammps wrapper classes in Python. These wrappers try to
+simplify the usage of LAMMPS in Python by providing an object-based interface
+to common LAMMPS functionality. It also reduces the amount of code necessary to
+parameterize LAMMPS scripts through Python and makes variables and computes
+directly accessible. See "PyLammps interface"_#py_9 for more details.
+
+Third, LAMMPS can use the Python interpreter, so that a LAMMPS input
 script can invoke Python code, and pass information back-and-forth
 between the input script and Python functions you write.  The Python
 code can also callback to LAMMPS to query or change its attributes.
 In Python lingo, this is "embedding" Python in LAMMPS.
 
-This section describes how to do both.
+This section describes how to use these three approaches.
 
 11.1 "Overview of running LAMMPS from Python"_#py_1
 11.2 "Overview of using Python from a LAMMPS script"_#py_2
@@ -29,7 +36,8 @@ This section describes how to do both.
 11.5 "Extending Python with MPI to run in parallel"_#py_5
 11.6 "Testing the Python-LAMMPS interface"_#py_6
 11.7 "Using LAMMPS from Python"_#py_7
-11.8 "Example Python scripts that use LAMMPS"_#py_8 :ul
+11.8 "Example Python scripts that use LAMMPS"_#py_8
+11.9 "PyLammps interface"_#py_9 :ul
 
 If you are not familiar with it, "Python"_http://www.python.org is a
 powerful scripting and programming language which can essentially do
@@ -89,7 +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
@@ -169,7 +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.
@@ -317,7 +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
@@ -361,7 +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
@@ -534,10 +542,11 @@ from lammps import lammps :pre
 These are the methods defined by the lammps module.  If you look at
 the files src/library.cpp and src/library.h you will see that they
 correspond one-to-one with calls you can make to the LAMMPS library
-from a C++ or C or Fortran program.
+from a C++ or C or Fortran program, and which are described in
+"Section 6.19"_Section_howto.html#howto_19 of the manual.
 
 lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
-                         4 optional args are allowed: name, cmdargs, ptr, comm
+                         # 4 optional args are allowed: name, cmdargs, ptr, comm
 lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
 lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
 lmp = lammps(name="g++")   # create a LAMMPS object using the liblammps_g++.so library
@@ -549,6 +558,8 @@ version = lmp.version()  # return the numerical version id, e.g. LAMMPS 2 Sep 20
 
 lmp.file(file)           # run an entire input script, file = "in.lj"
 lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100" :pre
+lmp.commands_list(cmdlist)     # invoke commands in cmdlist = ["run 10", "run 20"]
+lmp.commands_string(multicmd)  # invoke commands in multicmd = "run 10\nrun 20"
 
 xlo = lmp.extract_global(name,type)  # extract a global quantity
                                      # name = "boxxlo", "nlocal", etc
@@ -580,6 +591,8 @@ var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
                                              #        1 = atom-style variable :pre
 
 flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
+value = lmp.get_thermo(name)              # return current value of a thermo keyword
+
 natoms = lmp.get_natoms()                 # total # of atoms as int
 data = lmp.gather_atoms(name,type,count)  # return atom attribute of all atoms gathered into data, ordered by atom ID
                                           # name = "x", "charge", "type", etc
@@ -597,11 +610,12 @@ 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 can be used to tell Python the name of the shared
-library to load or to pass arguments to the LAMMPS instance, the same
-as if LAMMPS were launched from a command-line prompt.
+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
+instance, the same as if LAMMPS were launched from a command-line
+prompt.
 
 If the ptr argument is set like this:
 
@@ -626,8 +640,9 @@ lmp2 = lammps()
 lmp1.file("in.file1")
 lmp2.file("in.file2") :pre
 
-The file() and command() methods allow an input script or single
-commands to be invoked.
+The file(), command(), commands_list(), commands_string() methods
+allow an input script, a single command, or multiple commands to be
+invoked.
 
 The extract_global(), extract_atom(), extract_compute(),
 extract_fix(), and extract_variable() methods return values or
@@ -647,7 +662,7 @@ 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
@@ -759,7 +774,7 @@ 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)
 
@@ -817,3 +832,7 @@ different visualization package options.  Click to see larger images:
 :image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
 :image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
 :image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg)
+
+11.9 PyLammps interface :link(py_9),h4
+
+Please see the "PyLammps Tutorial"_tutorial_pylammps.html.

doc/src/Section_start.txt

@@ -80,7 +80,7 @@ This section has the following sub-sections:
 
 Read this first :h5,link(start_2_1)
 
-If you want to avoid building LAMMPS yourself, read the preceeding
+If you want to avoid building LAMMPS yourself, read the preceding
 section about options available for downloading and installing
 executables.  Details are discussed on the "download"_download page.
 
@@ -251,7 +251,7 @@ re-compile, after typing "make clean" (which will describe different
 clean options).
 
 The LMP_INC variable is used to include options that turn on ifdefs
-within the LAMMPS code.  The options that are currently recogized are:
+within the LAMMPS code.  The options that are currently recognized are:
 
 -DLAMMPS_GZIP
 -DLAMMPS_JPEG
@@ -362,7 +362,7 @@ installed on your platform.  If MPI is installed on your system in the
 usual place (under /usr/local), you also may not need to specify these
 3 variables, assuming /usr/local is in your path.  On some large
 parallel machines which use "modules" for their compile/link
-environements, you may simply need to include the correct module in
+environments, you may simply need to include the correct module in
 your build environment, before building LAMMPS.  Or the parallel
 machine may have a vendor-provided MPI which the compiler has no
 trouble finding.
@@ -413,7 +413,7 @@ 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
@@ -423,15 +423,14 @@ 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
 files.  Note that on some large parallel machines which use "modules"
-for their compile/link environements, you may simply need to include
+for their compile/link environments, you may simply need to include
 the correct module in your build environment.  Or the parallel machine
 may have a vendor-provided FFT library which the compiler has no
 trouble finding.
@@ -451,7 +450,7 @@ you must also manually specify the correct library, namely -lsfftw or
 
 The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
 use single-precision FFTs with PPPM, which can speed-up long-range
-calulations, particularly in parallel or on GPUs.  Fourier transform
+calculations, particularly in parallel or on GPUs.  Fourier transform
 and related PPPM operations are somewhat insensitive to floating point
 truncation errors and thus do not always need to be performed in
 double precision.  Using the -DFFT_SINGLE setting trades off a little
@@ -683,7 +682,7 @@ various make commands that can be used to manipulate 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
+Every command's doc page specifies if it is part of a package.  You can
 also type
 
 lmp_machine -h :pre
@@ -706,7 +705,7 @@ future changes to LAMMPS.
 User packages, such as user-atc or user-omp, have been contributed by
 users, and always begin with the user prefix.  If they are a single
 command (single file), they are typically in the user-misc package.
-Otherwise, they are a a set of files grouped together which add a
+Otherwise, they are a set of files grouped together which add a
 specific functionality to the code.
 
 User packages don't necessarily meet the requirements of the standard
@@ -1009,7 +1008,7 @@ 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
+The most recently executed Make.py command 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
@@ -1065,7 +1064,7 @@ src/MAKE/Makefile.foo and perform the build in the directory
 Obj_shared_foo.  This is so that each file can be compiled with the
 -fPIC flag which is required for inclusion in a shared library.  The
 build will create the file liblammps_foo.so which another application
-can link to dyamically.  It will also create a soft link liblammps.so,
+can link to dynamically.  It will also create a soft link liblammps.so,
 which will point to the most recently built shared library.  This is
 the file the Python wrapper loads by default.
 
@@ -1417,8 +1416,8 @@ LAMMPS is compiled with CUDA=yes.
 numa Nm :pre
 
 This option is only relevant when using pthreads with hwloc support.
-In this case Nm defines the number of NUMA regions (typicaly sockets)
-on a node which will be utilizied by a single MPI rank.  By default Nm
+In this case Nm defines the number of NUMA regions (typically sockets)
+on a node which will be utilized by a single MPI rank.  By default Nm
 = 1.  If this option is used the total number of worker-threads per
 MPI rank is threads*numa.  Currently it is always almost better to
 assign at least one MPI rank per NUMA region, and leave numa set to
@@ -1482,7 +1481,7 @@ replica runs on on one or a few processors.  Note that with MPI
 installed on a machine (e.g. your desktop), you can run on more
 (virtual) processors than you have physical processors.
 
-To run multiple independent simulatoins from one input script, using
+To run multiple independent simulations from one input script, using
 multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
 of the manual.  World- and universe-style "variables"_variable.html
 are useful in this context.
@@ -1601,9 +1600,9 @@ implementations, either by environment variables that specify how to
 order physical processors, or by config files that specify what
 physical processors to assign to each MPI rank.  The -reorder switch
 simply gives you a portable way to do this without relying on MPI
-itself.  See the "processors out"_processors command for how to output
-info on the final assignment of physical processors to the LAMMPS
-simulation domain.
+itself.  See the "processors out"_processors.html command for how
+to output info on the final assignment of physical processors to
+the LAMMPS simulation domain.
 
 -screen file :pre
 
@@ -1727,7 +1726,7 @@ thermodynamic state and a total run time for the simulation.  It then
 appends statistics about the CPU time and storage requirements for the
 simulation.  An example set of statistics is shown here:
 
-Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre
 
 Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
 97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
@@ -1757,14 +1756,14 @@ Ave special neighs/atom = 2.34032
 Neighbor list builds = 26
 Dangerous builds = 0 :pre
 
-The first section provides a global loop timing summary. The loop time
+The first section provides a global loop timing summary. The {loop time}
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
-continuations required and for comparing performance with other
-similar MD codes.  The CPU use line provides the CPU utilzation per
+continuations required and for comparing performance with other,
+similar MD codes.  The {CPU use} line provides the CPU utilization per
 MPI task; it should be close to 100% times the number of OpenMP
-threads (or 1). Lower numbers correspond to delays due to file I/O or
-insufficient thread utilization.
+threads (or 1 of no OpenMP). Lower numbers correspond to delays due
+to file I/O or insufficient thread utilization.
 
 The MPI task section gives the breakdown of the CPU run time (in
 seconds) into major categories:
@@ -1791,7 +1790,7 @@ is present that also prints the CPU utilization in percent. In
 addition, when using {timer full} and the "package omp"_package.html
 command are active, a similar timing summary of time spent in threaded
 regions to monitor thread utilization and load balance is provided. A
-new entry is the {Reduce} section, which lists the time spend in
+new entry is the {Reduce} section, which lists the time spent in
 reducing the per-thread data elements to the storage for non-threaded
 computation. These thread timings are taking from the first MPI rank
 only and and thus, as the breakdown for MPI tasks can change from MPI

doc/src/Section_tools.txt

@@ -471,7 +471,7 @@ These tools were written by Aidan Thompson at Sandia.
 restart2data tool :h4,link(restart)
 
 NOTE: This tool is now obsolete and is not included in the current
-LAMMPS distribution.  This is becaues there is now a
+LAMMPS distribution.  This is because 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:

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:]
 
@@ -29,7 +29,7 @@ Bond Styles: fene, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
-Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
+Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
 charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
 K-Space Styles: pppm :l
 :ule
@@ -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
@@ -151,7 +151,7 @@ can start running so that the CPU pipeline is still being used
 efficiently. Although benefits can be seen by launching a MPI task
 for every hardware thread, for multinode simulations, we recommend
 that OpenMP threads are used for SMT instead, either with the
-USER-INTEL package, "USER-OMP package"_accelerate_omp.html", or
+USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or
 "KOKKOS package"_accelerate_kokkos.html. In the example above, up
 to 36X speedups can be observed by using all 36 physical cores with
 LAMMPS. By using all 72 hardware threads, an additional 10-30%
@@ -343,7 +343,7 @@ when using offload.
 
 Not all styles are supported in the USER-INTEL package. You can mix
 the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
-package or the "USER-OMP package"_accelerate_omp.html". Of course,
+package or the "USER-OMP package"_accelerate_omp.html. Of course,
 this requires that these packages were installed at build time. This
 can performed automatically by using "-sf hybrid intel opt" or
 "-sf hybrid intel omp" command-line options. Alternatively, the "opt"
@@ -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

doc/src/accelerate_kokkos.txt

@@ -110,14 +110,14 @@ mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis :p
 [Required hardware/software:]
 
 Kokkos support within LAMMPS must be built with a C++11 compatible
-compiler.  If using gcc, version 4.8.1 or later is required.
+compiler.  If using gcc, version 4.7.2 or later is required.
 
 To build with Kokkos support for CPUs, your compiler must support the
 OpenMP interface.  You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.
 
 To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
-version 6.5 or later must be installed on your system.  See the
+version 7.5 or later must be installed on your system.  See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.
 
@@ -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_charmm.txt

@@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/angle_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_cosine.txt

@@ -61,7 +61,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/angle_cosine_delta.txt

@@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/angle_cosine_periodic.txt

@@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/angle_cosine_squared.txt

@@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/angle_harmonic.txt

@@ -65,11 +65,11 @@ more instructions on how to use the accelerated styles effectively.
 
 :line
 
-[Restrictions:] none
+[Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package.  See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.
 
 [Related commands:]
 

doc/src/angle_hybrid.txt

@@ -76,12 +76,12 @@ for specific angle types.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 Unlike other angle styles, the hybrid angle style does not store angle
 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_table.txt

@@ -147,7 +147,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/atom_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

@@ -115,7 +115,7 @@ particle.
 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 +149,7 @@ 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
@@ -165,8 +165,8 @@ 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
-defined via a molecule template using the "molecule"_molecule.txt
+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
 only store a template index and template atom to identify which
@@ -195,7 +195,7 @@ 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 +280,7 @@ 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_fene.txt

@@ -70,10 +70,10 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
-You typically should specify "special_bonds fene"_special_bonds.html"
+You typically should specify "special_bonds fene"_special_bonds.html
 or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
 style.  LAMMPS will issue a warning it that's not the case.
 

doc/src/bond_fene_expand.txt

@@ -73,10 +73,10 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
-You typically should specify "special_bonds fene"_special_bonds.html"
+You typically should specify "special_bonds fene"_special_bonds.html
 or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
 style.  LAMMPS will issue a warning it that's not the case.
 

doc/src/bond_harmonic.txt

@@ -65,7 +65,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/bond_hybrid.txt

@@ -59,12 +59,12 @@ bond types.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 Unlike other bond styles, the hybrid bond style does not store bond
 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_morse.txt

@@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/bond_nonlinear.txt

@@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/bond_oxdna.txt

@@ -0,0 +1,70 @@
+"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
+
+bond_style oxdna/fene command :h3
+
+[Syntax:]
+
+bond_style oxdna/fene :pre
+
+[Examples:]
+
+bond_style oxdna/fene
+bond_coeff * 2.0 0.25 0.7525 :pre
+
+[Description:]
+
+The {oxdna/fene} bond style uses the potential
+
+:c,image(Eqs/bond_oxdna_fene.jpg)
+
+to define a modified finite extensible nonlinear elastic (FENE) potential
+"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
+in the oxDNA force field for coarse-grained modelling of DNA. 
+
+The following coefficients must be defined for the bond type via the
+"bond_coeff"_bond_coeff.html command as given in the above example, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+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.html). 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/.
+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/.
+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.
+
+:line
+
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+
+[Related commands:]
+
+"pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
+
+[Default:] none
+
+:line
+
+:link(oxdna_fene)
+[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

doc/src/bond_quartic.txt

@@ -99,7 +99,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 The {quartic} style requires that "special_bonds"_special_bonds.html

doc/src/bond_table.txt

@@ -144,7 +144,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/bonds.txt

@@ -15,6 +15,7 @@ Bond Styles :h1
    bond_morse
    bond_none
    bond_nonlinear
+   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/commands.txt

@@ -37,6 +37,7 @@ Commands :h1
    dump_image
    dump_modify
    dump_molfile
+   dump_nc
    echo
    fix
    fix_modify
@@ -90,6 +91,7 @@ Commands :h1
    suffix
    tad
    temper
+   temper_grem
    thermo
    thermo_modify
    thermo_style

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_bond_local.txt

@@ -51,12 +51,12 @@ relative to the center of mass (COM) velocity of the 2 atoms in the
 bond.
 
 The value {engvib} is the vibrational kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and
+in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
 v2 are the magnitude of the velocity of the 2 atoms along the bond
 direction, after the COM velocity has been subtracted from each.
 
 The value {engrot} is the rotationsl kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and
+in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
 v2 are the magnitude of the velocity of the 2 atoms perpendicular to
 the bond direction, after the COM velocity has been subtracted from
 each.
@@ -67,7 +67,7 @@ Vcm^2 where Vcm = magnitude of the velocity of the COM.
 
 Note that these 3 kinetic energy terms are simply a partitioning of
 the summed kinetic energy of the 2 atoms themselves.  I.e. total KE =
-1/2 m1 v1^2 + 1/2 m2 v3^2 = engvib + engrot + engtrans, where v1,v2
+1/2 m1 v1^2 + 1/2 m2 v2^2 = engvib + engrot + engtrans, where v1,v2
 are the magnitude of the velocities of the 2 atoms, without any
 adjustment for the COM velocity.
 

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:]
@@ -108,13 +108,13 @@ 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
 they represent spatial directions.
 
-Here are typical centro-symmetry values, from a a nanoindentation
+Here are typical centro-symmetry values, from a nanoindentation
 simulation into gold (FCC).  These were provided by Jon Zimmerman
 (Sandia):
 

doc/src/compute_chunk_atom.txt

@@ -386,7 +386,7 @@ 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 +459,7 @@ 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
@@ -536,9 +536,9 @@ For the {bin/cylinder} style the details are as follows.  If {discard}
 is set to {yes}, an out-of-domain atom will have its chunk ID set to
 0.  If {discard} is set to {no}, the atom will have its chunk ID set
 to the first or last bin in both the radial and axis dimensions.  If
-{discard} is set to {mixed}, which is the default, the the radial
+{discard} is set to {mixed}, which is the default, the radial
 dimension is treated the same as for {discard} = no.  But for the axis
-dimensinon, it will only have its chunk ID set to the first or last
+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
@@ -641,7 +641,8 @@ the restarted simulation begins.
 
 [Related commands:]
 
-"fix ave/chunk"_fix_ave_chunk.html
+"fix ave/chunk"_fix_ave_chunk.html,
+"compute global/atom"_compute_global_atom.html
 
 [Default:]
 

doc/src/compute_cluster_atom.txt

@@ -37,7 +37,7 @@ The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
 is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each of a
-{clsuter/atom} style.
+{cluster/atom} style.
 
 NOTE: If you have a bonded system, then the settings of
 "special_bonds"_special_bonds.html command can remove pairwise

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

@@ -10,34 +10,43 @@ compute coord/atom command :h3
 
 [Syntax:]
 
-compute ID group-ID coord/atom cutoff type1 type2 ... :pre
+compute ID group-ID coord/atom cstyle args ... :pre
 
-ID, group-ID are documented in "compute"_compute.html command
-coord/atom = style name of this compute command
-cutoff = distance within which to count coordination neighbors (distance units)
-typeN = atom type for Nth coordination count (see asterisk form below) :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+coord/atom = style name of this compute command :l
+cstyle = {cutoff} or {orientorder} :l
+  {cutoff} args = cutoff typeN
+    cutoff = distance within which to count coordination neighbors (distance units)
+    typeN = atom type for Nth coordination count (see asterisk form below)
+  {orientorder} args = orientorderID threshold
+    orientorderID = ID of an orientorder/atom compute
+    threshold = minimum value of the product of two "connected" atoms :pre
+:ule
 
 [Examples:]
 
-compute 1 all coord/atom 2.0
-compute 1 all coord/atom 6.0 1 2
-compute 1 all coord/atom 6.0 2*4 5*8 * :pre
+compute 1 all coord/atom cutoff 2.0
+compute 1 all coord/atom cutoff 6.0 1 2
+compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
+compute 1 all coord/atom orientorder 2 0.5 :pre
 
 [Description:]
 
-Define a computation that calculates one or more coordination numbers
-for each atom in a group.
+This compute performs calculations between neighboring atoms to
+determine a coordination value.  The specific calculation and the
+meaning of the resulting value depend on the {cstyle} keyword used.
 
-A coordination number is defined as the number of neighbor atoms with
-specified atom type(s) that are within the specified cutoff distance
-from the central atom.  Atoms not in the group are included in a
-coordination number of atoms in the group.
+The {cutoff} cstyle calculates one or more traditional coordination
+numbers for each atom.  A coordination number is defined as the number
+of neighbor atoms with specified atom type(s) that are within the
+specified cutoff distance from the central atom.  Atoms not in the
+specified group are included in the coordination number tally.
 
-The {typeN} keywords allow you to specify which atom types contribute
-to each coordination number.  One coordination number is computed for
-each of the {typeN} keywords listed.  If no {typeN} keywords are
-listed, a single coordination number is calculated, which includes
-atoms of all types (same as the "*" format, see below).
+The {typeN} keywords allow specification of which atom types
+contribute to each coordination number.  One coordination number is
+computed for each of the {typeN} keywords listed.  If no {typeN}
+keywords are listed, a single coordination number is calculated, which
+includes atoms of all types (same as the "*" format, see below).
 
 The {typeN} keywords can be specified in one of two ways.  An explicit
 numeric value can be used, as in the 2nd example above.  Or a
@@ -49,8 +58,27 @@ from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).
 
-The value of all coordination numbers will be 0.0 for atoms not in the
-specified compute group.
+The {orientorder} cstyle calculates the number of "connected" neighbor
+atoms J around each central atom I.  For this {cstyle}, connected is
+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.
+
+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 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},
+then I and J are connected, and the coordination value of I is
+incremented by one.
+
+For all {cstyle} settings, all coordination values will be 0.0 for
+atoms not in the specified compute group.
 
 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@@ -72,11 +100,16 @@ the neighbor list.
 
 [Output info:]
 
-If single {type1} keyword is specified (or if none are specified),
-this compute calculates a per-atom vector.  If multiple {typeN}
-keywords are specified, this compute calculates a per-atom array, with
-N columns.  These values can be accessed by any command that uses
-per-atom values from a compute as input.  See "Section
+For {cstyle} cutoff, this compute can calculate a per-atom vector or
+array.  If single {type1} keyword is specified (or if none are
+specified), this compute calculates a per-atom vector.  If multiple
+{typeN} keywords are specified, this compute calculates a per-atom
+array, with N columns.
+
+For {cstyle} orientorder, this compute calculates a per-atom vector.
+
+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
 options.
 
@@ -88,5 +121,12 @@ explained above.
 [Related commands:]
 
 "compute cluster/atom"_compute_cluster_atom.html
+"compute orientorder/atom"_compute_orientorder_atom.html
 
 [Default:] none
+
+:line
+
+:link(tenWolde)
+[(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:]