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

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

doc/Makefile

@@ -22,7 +22,7 @@ endif
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub html pdf old venv
+.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
 
 # ------------------------------------------
 
@@ -36,6 +36,7 @@ help:
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
+	@echo "  anchor_check  scan for duplicate anchor labels"
 
 # ------------------------------------------
 
@@ -44,12 +45,19 @@ clean-all:
 
 clean:
 	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
@@ -64,6 +72,17 @@ html: $(OBJECTS)
 	@rm -rf html/USER/*/*.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
+spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
+	@(\
+		. $(VENV)/bin/activate ;\
+		pip install sphinxcontrib-spelling ;\
+		cp -r src/* $(RSTDIR)/ ;\
+        cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
+		sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
+		deactivate ;\
+	)
+	@echo "Spell check finished."
+
 epub: $(OBJECTS)
 	@mkdir -p epub
 	@rm -f LAMMPS.epub
@@ -112,6 +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/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/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/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="13 Feb 2017 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
-13 Feb 2017 version :c,h4
+17 Mar 2017 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -281,12 +281,12 @@ the "minimize"_minimize.html command.  A parallel tempering
 
 3.4 Commands listed by category :link(cmd_4),h4
 
-This section lists all LAMMPS commands, grouped by category.  The
+This section lists core LAMMPS commands, grouped by category.
-"next section"_#cmd_5 lists the same commands alphabetically.  The
+The "next section"_#cmd_5 lists all commands alphabetically.  The
 next section also includes (long) lists of style options for entries
 that appear in the following categories as a single command (fix,
 compute, pair, etc).  Commands that are added by user packages are not
-included in these categories, but they are in the next section.
+included in the categories here, but they are in the next section.
 
 Initialization:
 
@@ -361,7 +361,7 @@ Settings:
 "timer"_timer.html,
 "timestep"_timestep.html
 
-Operations within timestepping (fixes) and diagnositics (computes):
+Operations within timestepping (fixes) and diagnostics (computes):
 
 "compute"_compute.html,
 "compute_modify"_compute_modify.html,
@@ -687,6 +687,7 @@ package"_Section_start.html#start_3.
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
 "eos/table/rx"_fix_eos_table_rx.html,
+"filter/corotate"_fix_filter_corotate.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
 "grem"_fix_grem.html,
@@ -1016,6 +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,
@@ -1076,7 +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,
@@ -1091,7 +1093,7 @@ package"_Section_start.html#start_3.
 
 "harmonic/shift (o)"_bond_harmonic_shift.html,
 "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
+"oxdna/fene"_bond_oxdna.html :tb(c=4,ea=c)
 
 :line
 
@@ -1109,7 +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,
@@ -1145,7 +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,
@@ -1177,7 +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

@@ -574,11 +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
 
@@ -912,7 +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
@@ -992,7 +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
 
@@ -1327,7 +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
@@ -2005,7 +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
 
@@ -2088,7 +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
 
@@ -2131,7 +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
 
@@ -2291,7 +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
 
@@ -2641,11 +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
 
@@ -2706,15 +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
 
@@ -2735,11 +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
 
@@ -2747,7 +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
 
@@ -2760,7 +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
 
@@ -2790,7 +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
 
@@ -2835,7 +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
 
@@ -2881,11 +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
 
@@ -2935,7 +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
 
@@ -3079,7 +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
 
@@ -3524,12 +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
@@ -3638,7 +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
 
@@ -4385,7 +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
 
@@ -4617,11 +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
 
@@ -4970,7 +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
 
@@ -6171,7 +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
 
@@ -6199,7 +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
@@ -6463,15 +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
 
@@ -6737,7 +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
 
@@ -6751,7 +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
 
@@ -7313,7 +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
 
@@ -7361,7 +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
@@ -7526,7 +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
 
@@ -7552,7 +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
@@ -7792,7 +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
@@ -8042,7 +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
 
@@ -8663,7 +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
 
@@ -8948,11 +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
 
@@ -9166,7 +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
 
@@ -10025,7 +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
@@ -10087,7 +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
@@ -10155,7 +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
 
@@ -10654,7 +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
 
@@ -10666,7 +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
 
@@ -10707,7 +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
@@ -10796,7 +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
 
@@ -11083,7 +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
 
@@ -11414,7 +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
@@ -11452,7 +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
@@ -11537,7 +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
 
@@ -11589,7 +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
@@ -11886,7 +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
@@ -1888,7 +1892,7 @@ instances of LAMMPS to perform different calculations.
 
 The lammps_open_no_mpi() function is similar except that no MPI
 communicator is passed from the caller.  Instead, MPI_COMM_WORLD is
-used to instantiate LAMMPS, and MPI is initialzed if necessary.
+used to instantiate LAMMPS, and MPI is initialized if necessary.
 
 The lammps_close() function is used to shut down an instance of LAMMPS
 and free all its memory.
@@ -1976,7 +1980,7 @@ The lammps_get_natoms() function returns the total number of atoms in
 the system and can be used by the caller to allocate space for the
 lammps_gather_atoms() and lammps_scatter_atoms() functions.  The
 gather function collects atom info of the requested type (atom coords,
-types, forces, etc) from all procsesors, orders them by atom ID, and
+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.
@@ -2013,7 +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
 
@@ -2099,7 +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.
@@ -2125,7 +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
@@ -2268,7 +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.
@@ -2353,7 +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:
@@ -2424,7 +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
@@ -2444,7 +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).
@@ -2478,7 +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
@@ -2497,7 +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
@@ -2551,7 +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
@@ -2573,7 +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
@@ -2667,13 +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
+following issues should be considered.  The relative motion of
-the core and shell particles corresponds to the polarization, typical
+the core and shell particles corresponds to the polarization, 
-thermostats can alter the polarization behaviour, meaning the shell
+hereby an instantaneous relaxation of the shells is approximated 
-will not react freely to its electrostatic environment.  This is
+and a fast core/shell spring frequency ensures a nearly constant
-critical during the equilibration of the system. Therefore
+internal kinetic energy during the simulation. 
-it's typically desirable to decouple the relative motion of the
+Thermostats can alter this polarization behaviour, by scaling the
-core/shell pair, which is an imaginary degree of freedom, from the
+internal kinetic energy, meaning the shell will not react freely to 
+its electrostatic environment. 
+Therefore it is typically desirable to decouple the relative motion of 
+the core/shell pair, which is an imaginary degree of freedom, from the
 real physical system.  To do that, the "compute
 temp/cs"_compute_temp_cs.html command can be used, in conjunction with
 any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
@@ -2704,44 +2711,54 @@ fix thermostatequ all nve                               # integrator as needed f
 fix_modify thermoberendsen temp CSequ
 thermo_modify temp CSequ                                # output of center-of-mass derived temperature :pre
 
+The pressure for the core/shell system is computed via the regular 
+LAMMPS convention by "treating the cores and shells as individual 
+particles"_#MitchellFincham2. For the thermo output of the pressure 
+as well as for the application of a barostat, it is necessary to 
+use an additional "pressure"_compute_pressure compute based on the 
+default "temperature"_compute_temp and specifying it as a second 
+argument in "fix modify"_fix_modify.html and 
+"thermo_modify"_thermo_modify.html resulting in:
+
+(...)
+compute CSequ all temp/cs cores shells
+compute thermo_press_lmp all pressure thermo_temp       # pressure for individual particles
+thermo_modify temp CSequ press thermo_press_lmp         # modify thermo to regular pressure
+fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
+fix_modify press_bar temp CSequ press thermo_press_lmp  # pressure modification for correct kinetic scalar :pre
+
 If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
 relative motion of the core and the shell should in theory be
 stable.  However numerical fluctuation can introduce a small
 momentum to the system, which is noticable over long trajectories.
-Therefore it is recomendable to use the "fix
+Therefore it is recommendable to use the "fix
 momentum"_fix_momentum.html command in combination with "compute
 temp/cs"_compute_temp_cs.html when equilibrating the system to
 prevent any drift.
 
-When intializing the velocities of a system with core/shell pairs, it
+When initializing the velocities of a system with core/shell pairs, it
 is also desirable to not introduce energy into the relative motion of
 the core/shell particles, but only assign a center-of-mass velocity to
 the pairs.  This can be done by using the {bias} keyword of the
 "velocity create"_velocity.html command and assigning the "compute
 temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
-"velocity"_velocity.html commmand, e.g.
+"velocity"_velocity.html command, e.g.
 
 velocity all create 1427 134 bias yes temp CSequ
 velocity all scale 1427 temp CSequ :pre
 
-It is important to note that the polarizability of the core/shell
+To maintain the correct polarizability of the core/shell pairs, the 
-pairs is based on their relative motion. Therefore the choice of
+kinetic energy of the internal motion shall remain nearly constant. 
-spring force and mass ratio need to ensure much faster relative motion
+Therefore the choice of spring force and mass ratio need to ensure 
-of the 2 atoms within the core/shell pair than their center-of-mass
+much faster relative motion of the 2 atoms within the core/shell pair 
-velocity. This allow the shells to effectively react instantaneously
+than their center-of-mass velocity. This allows the shells to 
-to the electrostatic environment.  This fast movement also limits the
+effectively react instantaneously to the electrostatic environment and 
-timestep size that can be used.
+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
+energy transfer to the environment. 
-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 small drift
 in total energy over time.  This internal energy can be monitored
 using the "compute chunk/atom"_compute_chunk_atom.html and "compute
@@ -2761,14 +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
+(...) :pre
-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
 
 The additional section in the date file would be formatted like this:
 
@@ -2789,7 +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):
@@ -2890,9 +2913,13 @@ Phys, 79, 926 (1983).
 :link(Shinoda)
 [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
 
-:link(MitchellFinchham)
+:link(MitchellFincham)
-[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
+[(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_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

@@ -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
+Coulombics on one set of processors, and the remainder of the force
-field calcalation on another set.
+field calculation on another set.
 
 To install via make or Make.py:
 
@@ -1176,7 +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).
@@ -1295,13 +1295,13 @@ integrators with improved stability.
 
 See these doc pages to get started:
 
-"bond_style oxdna_fene"_bond_oxdna_fene.html
+"bond_style oxdna/fene"_bond_oxdna.html
-"pair_style oxdna_excv"_pair_oxdna_excv.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_fene.html, "pair_style
+oxdna/fene"_bond_oxdna.html, "pair_style
-oxdna_excv"_pair_oxdna_excv.html, "fix
+oxdna/..."_pair_oxdna.html, "fix
 nve/dotc/langevin"_fix_nve_dotc_langevin.html
 
 Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
@@ -1778,7 +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
@@ -1848,7 +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

@@ -97,7 +97,7 @@ current LAMMPS library interface and how to call them from Python.
 Section 11.8 gives some examples of coupling LAMMPS to other tools via
 Python.  For example, LAMMPS can easily be coupled to a GUI or other
 visualization tools that display graphs or animations in real time as
-LAMMPS runs.  Examples of such scripts are inlcluded in the python
+LAMMPS runs.  Examples of such scripts are included in the python
 directory.
 
 Two advantages of using Python to run LAMMPS are how concise the
@@ -177,7 +177,7 @@ of Python and your machine to successfully build LAMMPS.  See the
 lib/python/README file for more info.
 
 If you want to write Python code with callbacks to LAMMPS, then you
-must also follow the steps overviewed in the preceeding section (11.1)
+must also follow the steps overviewed in the preceding section (11.1)
 for running LAMMPS from Python.  I.e. you must build LAMMPS as a
 shared library and insure that Python can find the python/lammps.py
 file and the shared library.
@@ -325,7 +325,7 @@ sudo python setup.py install :pre
 Again, the "sudo" is only needed if required to copy PyPar files into
 your Python distribution's site-packages directory.
 
-If you have successully installed PyPar, you should be able to run
+If you have successfully installed PyPar, you should be able to run
 Python and type
 
 import pypar :pre
@@ -369,7 +369,7 @@ user privilege into the user local directory type
 
 python setup.py install --user :pre
 
-If you have successully installed mpi4py, you should be able to run
+If you have successfully installed mpi4py, you should be able to run
 Python and type
 
 from mpi4py import MPI :pre
@@ -610,7 +610,7 @@ lmp = lammps() :pre
 
 create an instance of LAMMPS, wrapped in a Python class by the lammps
 Python module, and return an instance of the Python class as lmp.  It
-is used to make all subequent calls to the LAMMPS library.
+is used to make all subsequent calls to the LAMMPS library.
 
 Additional arguments to lammps() can be used to tell Python the name
 of the shared library to load or to pass arguments to the LAMMPS
@@ -662,7 +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
@@ -774,7 +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)
 

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.
@@ -430,7 +430,7 @@ 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.
@@ -450,7 +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
@@ -682,7 +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
@@ -1008,7 +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
@@ -1064,7 +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.
 
@@ -1416,8 +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)
+In this case Nm defines the number of NUMA regions (typically sockets)
-on a node which will be utilizied by a single MPI rank.  By default Nm
+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
@@ -1481,7 +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.
@@ -1760,7 +1760,7 @@ 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
+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 of no OpenMP). Lower numbers correspond to delays due
 to file I/O or insufficient thread utilization.

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:]
 
@@ -115,7 +115,7 @@ coprocessor and an Intel compiler are required. For this, the
 recommended version of the Intel compiler is 14.0.1.106 or
 versions 15.0.2.044 and higher.
 
-Although any compiler can be used with the USER-INTEL pacakge,
+Although any compiler can be used with the USER-INTEL package,
 currently, vectorization directives are disabled by default when
 not using Intel compilers due to lack of standard support and
 observations of decreased performance. The OpenMP standard now
@@ -428,7 +428,7 @@ to the card.  This allows for overlap of MPI communication of forces
 with computation on the coprocessor when the "newton"_newton.html
 setting is "on".  The default is dependent on the style being used,
 however, better performance may be achieved by setting this option
-explictly.
+explicitly.
 
 When using offload with CPU Hyper-Threading disabled, it may help
 performance to use fewer MPI tasks and OpenMP threads than available

doc/src/accelerate_kokkos.txt

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

doc/src/angle_class2.txt

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

doc/src/angle_hybrid.txt

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

doc/src/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
@@ -165,7 +165,7 @@ For the {tri} style, the particles are planar triangles and each
 stores a per-particle mass and size and orientation (i.e. the corner
 points of the triangle).
 
-The {template} style allows molecular topolgy (bonds,angles,etc) to be
+The {template} style allows molecular topology (bonds,angles,etc) to be
 defined via a molecule template using the "molecule"_molecule.html
 command.  The template stores one or more molecules with a single copy
 of the topology info (bonds,angles,etc) of each.  Individual atoms
@@ -195,7 +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.
+one of the dimensions, leaving one new sub-box on either side of the
-All the processors are also partitioned into 2 groups, half assigned
+cut.  Which dimension is chosen for the cut depends on the particle
-to the box on the lower side of the cut, and half to the box on the
+(weight) distribution within the parent box.  Normally the longest
-upper side.  (If the processor count is odd, one side gets an extra
+dimension of the box is cut, but if all (or most) of the particles are
-processor.)  The cut is positioned so that the number of particles in
+at one end of the box, a cut may be performed in another dimension to
-the lower box is exactly the number that the processors assigned to
+induce sub-boxes that are more cube-ish (3d) or square-ish (2d) in
-that box should own for load balance to be perfect.  This also makes
+shape.
-load balance for the upper box perfect.  The positioning is done
+
-iteratively, by a bisectioning method.  Note that counting particles
+After the cut is made, all the processors are also partitioned into 2
-on either side of the cut requires communication between all
+groups, half assigned to the box on the lower side of the cut, and
-processors at each iteration.
+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
+assigned to each box make a new cut in one dimension of that box,
-box, splitting the box, the subset of processsors, and the particles
+splitting the box, the subset of processors, and the particles in the
-in the box in two.  The recursion continues until every processor is
+box in two.  The recursion continues until every processor is assigned
-assigned a sub-box of the entire simulation domain, and owns the
+a sub-box of the entire simulation domain, and owns the (weighted)
 particles in that sub-box.
 
 :line
@@ -368,7 +376,7 @@ of about 0.8 often results in the best performance, since the number
 of neighbors is likely to overestimate the ideal weight.
 
 This weight style is useful for systems where there are different
-cutoffs used for different pairs of interations, or the density
+cutoffs used for different pairs of interactions, or the density
 fluctuates, or a large number of particles are in the vicinity of a
 wall, or a combination of these effects.  If a simulation uses
 multiple neighbor lists, this weight style will use the first suitable
@@ -402,7 +410,7 @@ decrease the weights so that the ratio of max weight to min weight
 decreases by {factor}.  In both cases the intermediate weight values
 increase/decrease proportionally as well.  A value = 1.0 has no effect
 on the {time} weights.  As a rule of thumb, effective values to use
-are typicall between 0.5 and 1.2.  Note that the timer quantities
+are typically between 0.5 and 1.2.  Note that the timer quantities
 mentioned above can be affected by communication which occurs in the
 middle of the operations, e.g. pair styles with intermediate exchange
 of data witin the force computation, and likewise for KSpace solves.

doc/src/body.txt

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

doc/src/bond_class2.txt

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

doc/src/bond_hybrid.txt

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

doc/src/bond_oxdna.txt

@@ -6,20 +6,20 @@
 
 :line
 
-bond_style oxdna_fene command :h3
+bond_style oxdna/fene command :h3
 
 [Syntax:]
 
-bond_style oxdna_fene :pre
+bond_style oxdna/fene :pre
 
 [Examples:]
 
-bond_style oxdna_fene
+bond_style oxdna/fene
 bond_coeff * 2.0 0.25 0.7525 :pre
 
 [Description:]
 
-The {oxdna_fene} bond style uses the potential
+The {oxdna/fene} bond style uses the potential
 
 :c,image(Eqs/bond_oxdna_fene.jpg)
 
@@ -37,14 +37,14 @@ 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}
+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 
+and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of 
-"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients 
+"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/.
+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/.
+DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
 A technical report with more information on the model, the structure of the input file,
 the setup tool and the performance of the LAMMPS-implementation of oxDNA
 can be found "here"_PDF/USER-CGDNA-overview.pdf.
@@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]
 
-"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
+"pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
 
 [Default:] none
 

doc/src/bonds.txt

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

doc/src/change_box.txt

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

doc/src/comm_style.txt

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

doc/src/compute.txt

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

doc/src/compute_angmom_chunk.txt

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

doc/src/compute_centro_atom.txt

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

doc/src/compute_chunk_atom.txt

@@ -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
@@ -538,7 +538,7 @@ is set to {yes}, an out-of-domain atom will have its chunk ID set to
 to the first or last bin in both the radial and axis dimensions.  If
 {discard} is set to {mixed}, which is the default, the radial
 dimension is treated the same as for {discard} = no.  But for the axis
-dimensinon, it will only have its chunk ID set to the first or last
+dimension, it will only have its chunk ID set to the first or last
 bin if bins extend to the simulation box boundary in the axis
 dimension.  This is the case if the {bound} keyword settings are
 {lower} and {upper}, which is the default.  If the {bound} keyword

doc/src/compute_cna_atom.txt

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

doc/src/compute_com.txt

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

doc/src/compute_coord_atom.txt

@@ -70,7 +70,7 @@ The ID of the previously specified "compute
 orientorder/atom"_compute_orientorder/atom command is specified as
 {orientorderID}.  The compute must invoke its {components} option to
 calculate components of the {Ybar_lm} vector for each atoms, as
-described in its documenation.  Note that orientorder/atom compute
+described in its documentation.  Note that orientorder/atom compute
 defines its own criteria for identifying neighboring atoms.  If the
 scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
 orientorder/atom compute is larger than the specified {threshold},

doc/src/compute_damage_atom.txt

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

doc/src/compute_dilatation_atom.txt

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

doc/src/compute_displace_atom.txt

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

doc/src/compute_event_displace.txt

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

doc/src/compute_global_atom.txt

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

doc/src/compute_heat_flux.txt

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

doc/src/compute_inertia_chunk.txt

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

doc/src/compute_msd.txt

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

doc/src/compute_msd_chunk.txt

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

doc/src/compute_msd_nongauss.txt

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

doc/src/compute_pair.txt

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

doc/src/compute_pair_local.txt

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

doc/src/compute_pe_atom.txt

@@ -51,7 +51,7 @@ these terms is included in the pair energy, not the dihedral energy.
 The KSpace contribution is calculated using the method in
 "(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
 as specified by the "kspace_style pppm"_kspace_style.html command.
-For PPPM, the calcluation requires 1 extra FFT each timestep that
+For PPPM, the calculation requires 1 extra FFT each timestep that
 per-atom energy is calculated.  This "document"_PDF/kspace.pdf
 describes how the long-range per-atom energy calculation is performed.
 

doc/src/compute_plasticity_atom.txt

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

doc/src/compute_pressure.txt

@@ -89,7 +89,7 @@ commands"_compute.html to determine which ones include a bias.
 
 Also note that the N in the first formula above is really
 degrees-of-freedom divided by d = dimensionality, where the DOF value
-is calcluated by the temperature compute.  See the various "compute
+is calculated by the temperature compute.  See the various "compute
 temperature"_compute.html styles for details.
 
 A compute of this style with the ID of "thermo_press" is created when

doc/src/compute_property_chunk.txt

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

doc/src/compute_rdf.txt

@@ -10,21 +10,27 @@ compute rdf command :h3
 
 [Syntax:]
 
-compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... :pre
+compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... keyword/value ... :pre
 
-ID, group-ID are documented in "compute"_compute.html command
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
-rdf = style name of this compute command
+rdf = style name of this compute command :l
-Nbin = number of RDF bins
+Nbin = number of RDF bins :l
-itypeN = central atom type for Nth RDF histogram (see asterisk form below)
+itypeN = central atom type for Nth RDF histogram (see asterisk form below) :l
-jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) :ul
+jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) :l
+
+zero or more keyword/value pairs may be appended :l
+keyword = {cutoff} :l
+  {cutoff} value = Rcut
+    Rcut = cutoff distance for RDF computation (distance units) :pre
+:ule
 
 [Examples:]
 
 compute 1 all rdf 100
 compute 1 all rdf 100 1 1
-compute 1 all rdf 100 * 3
+compute 1 all rdf 100 * 3 cutoff 5.0
 compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
-compute 1 fluid rdf 500 1*3 2 5 *10 :pre
+compute 1 fluid rdf 500 1*3 2 5 *10 cutoff 3.5 :pre
 
 [Description:]
 
@@ -32,7 +38,8 @@ Define a computation that calculates the radial distribution function
 (RDF), also called g(r), and the coordination number for a group of
 particles.  Both are calculated in histogram form by binning pairwise
 distances into {Nbin} bins from 0.0 to the maximum force cutoff
-defined by the "pair_style"_pair_style.html command.  The bins are of
+defined by the "pair_style"_pair_style.html command or the cutoff
+distance {Rcut} specified via the {cutoff} keyword.  The bins are of
 uniform size in radial distance.  Thus a single bin encompasses a thin
 shell of distances in 3d and a thin ring of distances in 2d.
 
@@ -52,6 +59,30 @@ the dump file.  The rerun script can use a
 "special_bonds"_special_bonds.html command that includes all pairs in
 the neighbor list.
 
+By default the RDF is computed out to the maximum force cutoff defined
+by the "pair_style"_pair_style.html command.  If the {cutoff} keyword
+is used, then the RDF is computed accurately out to the {Rcut} > 0.0
+distance specified.
+
+NOTE: Normally, you should only use the {cutoff} keyword if no pair
+style is defined, e.g. the "rerun"_rerun.html command is being used to
+post-process a dump file of snapshots.  Or if you really want the RDF
+for distances beyond the pair_style force cutoff and cannot easily
+post-process a dump file to calculate it.  This is because using the
+{cutoff} keyword incurs extra computation and possibly communication,
+which may slow down your simulation.  If you specify a {Rcut} <= force
+cutoff, you will force an additional neighbor list to be built at
+every timestep this command is invoked (or every reneighboring
+timestep, whichever is less frequent), which is inefficient.  LAMMPS
+will warn you if this is the case.  If you specify a {Rcut} > force
+cutoff, you must insure ghost atom information out to {Rcut} + {skin}
+is communicated, via the "comm_modify cutoff"_comm_modify.html
+command, else the RDF computation cannot be performed, and LAMMPS will
+give an error message.  The {skin} value is what is specified with the
+"neighbor"_neighbor.html command.  In this case, you are forcing a
+large neighbor list to be built just for the RDF computation, and
+extra communication to be performed every timestep.
+
 The {itypeN} and {jtypeN} arguments are optional.  These arguments
 must come in pairs.  If no pairs are listed, then a single histogram
 is computed for g(r) between all atom types.  If one or more pairs are
@@ -153,4 +184,6 @@ change from zero to one at the location of the spike in g(r).
 
 "fix ave/time"_fix_ave_time.html
 
-[Default:] none
+[Default:]
+
+The keyword defaults are cutoff = 0.0 (use the pairwise force cutoff).

doc/src/compute_rigid_local.txt

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

doc/src/compute_saed.txt

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

doc/src/compute_smd_ulsph_num_neighs.txt

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

doc/src/compute_stress_atom.txt

@@ -92,7 +92,7 @@ The KSpace contribution is calculated using the method in
 "(Heyes)"_#Heyes for the Ewald method and by the methodology described
 in "(Sirk)"_#Sirk for PPPM.  The choice of KSpace solver is specified
 by the "kspace_style pppm"_kspace_style.html command.  Note that for
-PPPM, the calcluation requires 6 extra FFTs each timestep that
+PPPM, the calculation requires 6 extra FFTs each timestep that
 per-atom stress is calculated.  Thus it can significantly increase the
 cost of the PPPM calculation if it is needed on a large fraction of
 the simulation timesteps.

doc/src/compute_temp_asphere.txt

@@ -138,7 +138,7 @@ This compute is part of the ASPHERE package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This compute requires that atoms store angular momementum and a
+This compute requires that atoms store angular momentum and a
 quaternion as defined by the "atom_style ellipsoid"_atom_style.html
 command.
 

doc/src/compute_temp_body.txt

@@ -120,7 +120,7 @@ This compute is part of the BODY package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This compute requires that atoms store angular momementum and a
+This compute requires that atoms store angular momentum and a
 quaternion as defined by the "atom_style body"_atom_style.html
 command.
 

doc/src/compute_temp_chunk.txt

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

doc/src/compute_temp_profile.txt

@@ -118,7 +118,7 @@ needed, the subtracted degrees-of-freedom can be altered using the
 
 NOTE: When using the {out} keyword with a value of {bin}, the
 calculated temperature for each bin does not include the
-degrees-of-freedom adjustment described in the preceeding paragraph,
+degrees-of-freedom adjustment described in the preceding paragraph,
 for fixes that constrain molecular motion.  It does include the
 adjustment due to the {extra} option, which is applied to each bin.
 

doc/src/compute_vacf.txt

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

doc/src/compute_voronoi_atom.txt

@@ -217,6 +217,10 @@ This compute is part of the VORONOI package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
+It also requiers you have a copy of the Voro++ library built and
+installed on your system.  See instructions on obtaining and
+installing the Voro++ software in the src/VORONOI/README file.
+
 [Related commands:]
 
 "dump custom"_dump.html, "dump local"_dump.html

doc/src/create_atoms.txt

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

doc/src/dihedral_class2.txt

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

doc/src/dihedral_hybrid.txt

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

doc/src/dump.txt

@@ -225,7 +225,7 @@ This bounding box is convenient for many visualization programs.  The
 meaning of the 6 character flags for "xx yy zz" is the same as above.
 
 Note that the first two numbers on each line are now xlo_bound instead
-of xlo, etc, since they repesent a bounding box.  See "this
+of xlo, etc, since they represent a bounding box.  See "this
 section"_Section_howto.html#howto_12 of the doc pages for a geometric
 description of triclinic boxes, as defined by LAMMPS, simple formulas
 for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
@@ -545,7 +545,7 @@ that the coordinate values may be far outside the box bounds printed
 with the snapshot.  Using {xsu}, {ysu}, {zsu} is similar to using
 {xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by
 the box size. Atoms that have passed through a periodic boundary will
-have the corresponding cooordinate increased or decreased by 1.0.
+have the corresponding coordinate increased or decreased by 1.0.
 
 The image flags can be printed directly using the {ix}, {iy}, {iz}
 attributes.  For periodic dimensions, they specify which image of the

doc/src/dump_custom_vtk.txt

@@ -211,7 +211,7 @@ charge.
 There are several options for outputting atom coordinates.  The {x},
 {y}, {z} attributes are used to write atom coordinates "unscaled", in
 the appropriate distance "units"_units.html (Angstroms, sigma, etc).
-Additionaly, you can use {xs}, {ys}, {zs} if you want to also save the
+Additionally, you can use {xs}, {ys}, {zs} if you want to also save the
 coordinates "scaled" to the box size, so that each value is 0.0 to
 1.0.  If the simulation box is triclinic (tilted), then all atom
 coords will still be between 0.0 and 1.0.  Use {xu}, {yu}, {zu} if you
@@ -224,7 +224,7 @@ values may be far outside the box bounds printed with the snapshot.
 Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except
 that the unwrapped coordinates are scaled by the box size. Atoms that
 have passed through a periodic boundary will have the corresponding
-cooordinate increased or decreased by 1.0.
+coordinate increased or decreased by 1.0.
 
 The image flags can be printed directly using the {ix}, {iy}, {iz}
 attributes.  For periodic dimensions, they specify which image of the

doc/src/dump_image.txt

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

doc/src/dump_modify.txt

@@ -426,7 +426,7 @@ regions.
 
 The {scale} keyword applies only to the dump {atom} style.  A scale
 value of {yes} means atom coords are written in normalized units from
-0.0 to 1.0 in each box dimension.  If the simluation box is triclinic
+0.0 to 1.0 in each box dimension.  If the simulation box is triclinic
 (tilted), then all atom coords will still be between 0.0 and 1.0.  A
 value of {no} means they are written in absolute distance units
 (e.g. Angstroms or sigma).
@@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold.
 
 If an atom-style variable is used as the attribute, then it can
 produce continuous numeric values or effective Boolean 0/1 values
-which may be useful for the comparision operator.  Boolean values can
+which may be useful for the comparison operator.  Boolean values can
 be generated by variable formulas that use comparison or Boolean math
 operators or special functions like gmask() and rmask() and grmask().
 See the "variable"_variable.html command doc page for details.

doc/src/fix_ave_chunk.txt

@@ -67,7 +67,7 @@ fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre
 
 [NOTE:]
 
-If you are trying to replace a deprectated fix ave/spatial command
+If you are trying to replace a deprecated fix ave/spatial command
 with the newer, more flexible fix ave/chunk and "compute
 chunk/atom"_compute_chunk_atom.html commands, you simply need to split
 the fix ave/spatial arguments across the two new commands.  For
@@ -189,7 +189,7 @@ chunk/atom"_compute_chunk_atom.html command must remain constant.  If
 the {ave} keyword is set to {running} or {window} then {Nchunk} must
 remain constant for the duration of the simulation.  This fix forces
 the chunk/atom compute specified by chunkID to hold {Nchunk} constant
-for the appropriate time windows, by not allowing it to re-calcualte
+for the appropriate time windows, by not allowing it to re-calculate
 {Nchunk}, which can also affect how it assigns chunk IDs to atoms.
 More details are given on the "compute
 chunk/atom"_compute_chunk_atom.html doc page.
@@ -301,7 +301,7 @@ sample values" divided by {Nrepeat}.  In other words it is an average
 of an average.
 
 If the {norm} setting is {none}, a similar computation as for the
-{sample} seting is done, except the individual "average sample values"
+{sample} setting is done, except the individual "average sample values"
 are "summed sample values".  A summed sample value is simply the chunk
 value summed over atoms in the sample, without dividing by the number
 of atoms in the sample.  The output value for the chunk on the
@@ -410,7 +410,7 @@ chunk/atom"_compute_chunk_atom.html command supports them.  The OrigID
 column is only used if the {compress} keyword was set to {yes} for the
 "compute chunk/atom"_compute_chunk_atom.html command.  This means that
 the original chunk IDs (e.g. molecule IDs) will have been compressed
-to remove chunk IDs with no atoms assigned to them.  Thus a compresed
+to remove chunk IDs with no atoms assigned to them.  Thus a compressed
 chunk ID of 3 may correspond to an original chunk ID or molecule ID of
 415.  The OrigID column will list 415 for the 3rd chunk.
 

doc/src/fix_ave_correlate.txt

@@ -64,7 +64,7 @@ fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\]
 [Description:]
 
 Use one or more global scalar values as inputs every few timesteps,
-calculate time correlations bewteen them at varying time intervals,
+calculate time correlations between them at varying time intervals,
 and average the correlation data over longer timescales.  The
 resulting correlation values can be time integrated by
 "variables"_variable.html or used by other "output
@@ -219,7 +219,7 @@ to {upper} then each input value is correlated with every succeeding
 value.  I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. :l
 
 If {type} is set
-to {lower} then each input value is correlated with every preceeding
+to {lower} then each input value is correlated with every preceding
 value.  I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. :l
 
 If {type} is set to {auto/upper} then each input value is correlated

doc/src/fix_ave_time.txt

@@ -33,7 +33,7 @@ keyword = {mode} or {file} or {ave} or {start} or {off} or {overwrite} or {title
     vector = all input values are global vectors or global arrays
   {ave} args = {one} or {running} or {window M}
     one = output a new average value every Nfreq steps
-    running = output cummulative average of all previous Nfreq steps
+    running = output cumulative average of all previous Nfreq steps
     window M = output average of M most recent Nfreq steps
   {start} args = Nstart
     Nstart = start averaging on this timestep
@@ -223,7 +223,7 @@ output as-is without further averaging.
 
 If the {ave} setting is {running}, then the values produced on
 timesteps that are multiples of {Nfreq} are summed and averaged in a
-cummulative sense before being output.  Each output value is thus the
+cumulative sense before being output.  Each output value is thus the
 average of the value produced on that timestep with all preceding
 values.  This running average begins when the fix is defined; it can
 only be restarted by deleting the fix via the "unfix"_unfix.html
@@ -320,7 +320,7 @@ input values are averaged and {mode} = vector.  The global array has #
 of rows = length of the input vectors and # of columns = number of
 inputs.
 
-If the fix prouduces a scalar or vector, then the scalar and each
+If the fix produces a scalar or vector, then the scalar and each
 element of the vector can be either "intensive" or "extensive",
 depending on whether the values contributing to the scalar or vector
 element are "intensive" or "extensive".  If the fix produces an array,

doc/src/fix_balance.txt

@@ -15,12 +15,12 @@ fix ID group-ID balance Nfreq thresh style args keyword args ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 balance = style name of this fix command :l
 Nfreq = perform dynamic load balancing every this many steps :l
-thresh = imbalance threshhold that must be exceeded to perform a re-balance :l
+thresh = imbalance threshold that must be exceeded to perform a re-balance :l
 style = {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
@@ -63,14 +63,14 @@ perform "static" balancing, before or between runs, see the
 
 Load-balancing is typically most useful if the particles in the
 simulation box have a spatially-varying density distribution or
-where the computational cost varies signficantly between different
+where the computational cost varies significantly between different
 atoms. 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 numbers of particles per processor in a
+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.
 
@@ -78,7 +78,7 @@ 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.
 
 NOTE: The weighting options listed above are documented with the
@@ -216,7 +216,7 @@ for a single value, except that the bounds used for each bisectioning
 take advantage of information from neighboring cuts if possible, as
 well as counts of particles at the bounds on either side of each cuts,
 which themselves were cuts in previous iterations.  The latter is used
-to infer a density of pariticles near each of the current cuts.  At
+to infer a density of particles near each of the current cuts.  At
 each iteration, the count of particles on either side of each plane is
 tallied.  If the counts do not match the target value for the plane,
 the position of the cut is adjusted based on the local density.  The
@@ -239,7 +239,7 @@ assigned, particles migrate to their new owning processor as part of
 the normal reneighboring procedure.
 
 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 based on the local density, as
 described above, which should typically be 1/2 or more every
@@ -249,7 +249,7 @@ typically be positioned to better than 1 part in 1000 accuracy
 be accurate to better than 1 part in a million.  Thus there is no need
 to set {Niter} to a large value.  This is especially true if you are
 rebalancing often enough that each time you expect only an incremental
-adjustement in the cutting planes is necessary.  LAMMPS will check if
+adjustment in the cutting planes is necessary.  LAMMPS will check if
 the threshold accuracy is reached (in a dimension) is less iterations
 than {Niter} and exit early.
 
@@ -275,7 +275,7 @@ 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 atoms in
+box, splitting the box, the subset of processors, and the atoms in
 the box in two.  The recursion continues until every processor is
 assigned a sub-box of the entire simulation domain, and owns the atoms
 in that sub-box.

doc/src/fix_bond_break.txt

@@ -79,8 +79,8 @@ part of bonds, angles, etc.
 
 NOTE: One data structure that is not updated when a bond breaks are
 the molecule IDs stored by each atom.  Even though one molecule
-becomes two moleclues due to the broken bond, all atoms in both new
+becomes two molecules due to the broken bond, all atoms in both new
-moleclues retain their original molecule IDs.
+molecules retain their original molecule IDs.
 
 Computationally, each timestep this fix operates, it loops over all
 the bonds in the system and computes distances between pairs of bonded
@@ -122,7 +122,7 @@ by this fix are "intensive".
 These are the 2 quantities:
 
 (1) # of bonds broken on the most recent breakage timestep
-(2) cummulative # of bonds broken :ul
+(2) cumulative # of bonds broken :ul
 
 No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy

doc/src/fix_bond_create.txt

@@ -118,8 +118,8 @@ of new bonds, angles, etc.
 
 NOTE: One data structure that is not updated when a bond breaks are
 the molecule IDs stored by each atom.  Even though two molecules
-become one moleclue due to the created bond, all atoms in the new
+become one molecule due to the created bond, all atoms in the new
-moleclue retain their original molecule IDs.
+molecule retain their original molecule IDs.
 
 If the {atype} keyword is used and if an angle potential is defined
 via the "angle_style"_angle_style.html command, then any new 3-body
@@ -218,7 +218,7 @@ by this fix are "intensive".
 These are the 2 quantities:
 
 (1) # of bonds created on the most recent creation timestep
-(2) cummulative # of bonds created :ul
+(2) cumulative # of bonds created :ul
 
 No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy

doc/src/fix_bond_swap.txt

@@ -81,7 +81,7 @@ by this processor on this timestep.
 The criterion for matching molecule IDs is how bond swaps performed by
 this fix conserve chain length.  To use this features you must setup
 the molecule IDs for your polymer chains in a certain way, typically
-in the data file, read by the "read_data"_read_data.html comand.
+in the data file, read by the "read_data"_read_data.html command.
 Consider a system of 6-mer chains.  You have 2 choices.  If the
 molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
 swaps will conserve chain length.  For a particular momoner there will
@@ -124,7 +124,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
 This means you can change the attributes of this fix's temperature
 (e.g. its degrees-of-freedom) via the
 "compute_modify"_compute_modify.html command or print this temperature
-during thermodyanmic output via the "thermo_style
+during thermodynamic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} will have no
 effect on this fix.
@@ -151,8 +151,8 @@ the Boltzmann criterion.
 This fix computes two statistical quantities as a global 2-vector of
 output, which can be accessed by various "output
 commands"_Section_howto.html#howto_15.  The first component of the
-vector is the cummulative number of swaps performed by all processors.
+vector is the cumulative number of swaps performed by all processors.
-The second component of the vector is the cummulative number of swaps
+The second component of the vector is the cumulative number of swaps
 attempted (whether accepted or rejected).  Note that a swap "attempt"
 only occurs when swap partners meeting the criteria described above
 are found on a particular timestep.  The vector values calculated by
@@ -168,7 +168,7 @@ This fix is part of the MC package.  It is only enabled if LAMMPS was
 built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-The setings of the "special_bond" command must be 0,1,1 in order to
+The settings of the "special_bond" command must be 0,1,1 in order to
 use this fix, which is typical of bead-spring chains with FENE or
 harmonic bonds.  This means that pairwise interactions between bonded
 atoms are turned off, but are turned on between atoms two or three

doc/src/fix_box_relax.txt

@@ -54,7 +54,7 @@ The external pressure tensor is specified using one or more of the
 keywords.  These keywords give you the ability to specify all 6
 components of an external stress tensor, and to couple various of
 these components together so that the dimensions they represent are
-varied together during the mimimization.
+varied together during the minimization.
 
 Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
 Triclinic (non-orthogonal) simulation boxes have 6 adjustable
@@ -103,7 +103,7 @@ far. In all cases, the particle positions at each iteration are
 unaffected by the chosen value, except that all particles are
 displaced by the same amount, different on each iteration.
 
-NOTE: Appling an external pressure to tilt dimensions {xy}, {xz}, {yz}
+NOTE: Applying an external pressure to tilt dimensions {xy}, {xz}, {yz}
 can sometimes result in arbitrarily large values of the tilt factors,
 i.e. a dramatically deformed simulation box.  This typically indicates
 that there is something badly wrong with how the simulation was
@@ -122,7 +122,7 @@ well-defined minimization problem.  This is because the objective
 function being minimized changes if the box size/shape changes.  In
 practice this means the minimizer can get "stuck" before you have
 reached the desired tolerance.  The solution to this is to restart the
-minmizer from the new adjusted box size/shape, since that creates a
+minimizer from the new adjusted box size/shape, since that creates a
 new objective function valid for the new box size/shape.  Repeat as
 necessary until the box size/shape has reached its new equilibrium.
 

doc/src/fix_cmap.txt

@@ -44,7 +44,7 @@ lammps/potentials directory: charmm22.cmap and charmm36.cmap.
 
 The data file read by the "read_data" must contain the topology of all
 the CMAP interactions, similar to the topology data for bonds, angles,
-dihedrals, etc.  Specically it should have a line like this
+dihedrals, etc.  Specially it should have a line like this
 in its header section:
 
 N crossterms :pre

doc/src/fix_colvars.txt

@@ -59,7 +59,7 @@ always apply to the entire system and there can only be one instance
 of the colvars fix at a time. The colvars fix will only communicate
 the minimum information necessary and the colvars library supports
 multiple, completely independent collective variables, so there is
-no restriction to functionaliry by limiting the number of colvars fixes.
+no restriction to functionality by limiting the number of colvars fixes.
 
 The {input} keyword allows to specify a state file that would contain
 the restart information required in order to continue a calculation from
@@ -100,7 +100,7 @@ output"_thermo_style.html.
 
 This fix computes a global scalar which can be accessed by various
 "output commands"_Section_howto.html#howto_15.  The scalar is the
-cummulative energy change due to this fix.  The scalar value
+cumulative energy change due to this fix.  The scalar value
 calculated by this fix is "extensive".
 
 [Restrictions:]

doc/src/fix_controller.txt

@@ -107,7 +107,7 @@ When choosing the values of the four constants, it is best to first
 pick a value and sign for {alpha} that is consistent with the
 magnitudes and signs of {pvar} and {cvar}.  The magnitude of {Kp}
 should then be tested over a large positive range keeping {Ki}={Kd}=0.
-A good value for {Kp} will produce a fast reponse in {pvar}, without
+A good value for {Kp} will produce a fast response in {pvar}, without
 overshooting the {setpoint}.  For many applications, proportional
 feedback is sufficient, and so {Ki}={Kd}=0 can be used. In cases where
 there is a substantial lag time in the response of {pvar} to a change
@@ -175,7 +175,7 @@ equal-style versus internal-style variable interchangeably.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-Currenlty, no information about this fix is written to "binary restart
+Currently, no information about this fix is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
 are relevant to this fix.
 

doc/src/fix_deform.txt

@@ -580,10 +580,10 @@ This fix is not invoked during "energy minimization"_minimize.html.
 [Restrictions:]
 
 You cannot apply x, y, or z deformations to a dimension that is
-shrink-wrapped via the "boundary"_boundary.html comamnd.
+shrink-wrapped via the "boundary"_boundary.html command.
 
 You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in
-xy) that is shrink-wrapped via the "boundary"_boundary.html comamnd.
+xy) that is shrink-wrapped via the "boundary"_boundary.html command.
 
 [Related commands:]
 

doc/src/fix_deposit.txt

@@ -15,7 +15,7 @@ fix ID group-ID deposit N type M seed keyword values ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 deposit = style name of this fix command :l
 N = # of atoms or molecules to insert :l
-type = atom type to assign to inserted atoms (offset for moleclue insertion) :l
+type = atom type to assign to inserted atoms (offset for molecule insertion) :l
 M = insert a single atom or molecule every M steps :l
 seed = random # seed (positive integer) :l
 one or more keyword/value pairs may be appended to args :l
@@ -140,7 +140,7 @@ the molecule.
 
 If the molecule template contains more than one molecule, the relative
 probability of depositing each molecule can be specified by the
-{molfrac} keyword.  N relative probablities, each from 0.0 to 1.0, are
+{molfrac} keyword.  N relative probabilities, each from 0.0 to 1.0, are
 specified, where N is the number of molecules in the template.  Each
 time a molecule is deposited, a random number is used to sample from
 the list of relative probabilities.  The N values must sum to 1.0.
@@ -192,7 +192,7 @@ LAMMPS prints a warning message.
 NOTE: If you are inserting finite size particles or a molecule or
 rigid body consisting of finite-size particles, then you should
 typically set R larger than the distance at which any inserted
-particle may overlap with either a previouly inserted particle or an
+particle may overlap with either a previously inserted particle or an
 existing particle.  LAMMPS will issue a warning if R is smaller than
 this value, based on the radii of existing and inserted particles.
 

doc/src/fix_eos_table.txt

@@ -17,7 +17,7 @@ eos/table = style name of this fix command
 style = {linear} = method of interpolation
 file = filename containing the tabulated equation of state
 N = use N values in {linear} tables
-keyword = name of table keyword correponding to table file :ul
+keyword = name of table keyword corresponding to table file :ul
 
 [Examples:]
 

doc/src/fix_eos_table_rx.txt

@@ -17,7 +17,7 @@ eos/table/rx = style name of this fix command
 style = {linear} = method of interpolation
 file1 = filename containing the tabulated equation of state
 N = use N values in {linear} tables
-keyword = name of table keyword correponding to table file
+keyword = name of table keyword corresponding to table file
 file2 = filename containing the heats of formation of each species (optional)
 deltaHf = heat of formation for a single species in energy units (optional)
 energyCorr = energy correction in energy units (optional)

doc/src/fix_evaporate.txt

@@ -31,9 +31,9 @@ fix 1 solvent evaporate 1000 10 surface 38277 molecule yes :pre
 [Description:]
 
 Remove M atoms from the simulation every N steps.  This can be used,
-for example, to model evaporation of solvent particles or moleclues
+for example, to model evaporation of solvent particles or molecules
 (i.e. drying) of a system.  Every N steps, the number of atoms in the
-fix group and within the specifed region are counted.  M of these are
+fix group and within the specified region are counted.  M of these are
 chosen at random and deleted.  If there are less than M eligible
 particles, then all of them are deleted.
 
@@ -74,7 +74,7 @@ are relevant to this fix.
 
 This fix computes a global scalar, which can be accessed by various
 "output commands"_Section_howto.html#howto_15.  The scalar is the
-cummulative number of deleted atoms.  The scalar value calculated by
+cumulative number of deleted atoms.  The scalar value calculated by
 this fix is "intensive".
 
 No parameter of this fix can be used with the {start/stop} keywords of

doc/src/fix_filter_corotate.txt

@@ -0,0 +1,87 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix filter/corotate command :h3
+
+[Syntax:]
+
+fix ID group-ID filter/corotate keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+one or more constraint/value pairs are appended :l
+constraint = {b} or {a} or {t} or {m} :l
+  {b} values = one or more bond types
+  {a} values = one or more angle types
+  {t} values = one or more atom types
+  {m} value = one or more mass values :pre
+:ule
+
+[Examples:]
+
+timestep 8
+run_style respa 3 2 8 bond 1 pair 2 kspace 3
+fix cor all filter/corotate m 1.0 :pre
+
+fix cor all filter/corotate b 4 19 a 3 5 2 :pre
+
+[Description:]
+
+This fix implements a corotational filter for a mollified impulse
+method. In biomolecular simulations, it allows the usage of larger
+timesteps for long-range electrostatic interactions.  For details, see
+"(Fath)"_#Fath2017.
+
+When using "run_style respa"_run_style.html for a biomolecular
+simulation with high-frequency covalent bonds, the outer time-step is
+restricted to below ~ 4fs due to resonance problems. This fix filters
+the outer stage of the respa and thus a larger (outer) time-step can
+be used. Since in large biomolecular simulations the computation of
+the long-range electrostatic contributions poses a major bottleneck,
+this can significantly accelerate the simulation.
+
+The filter computes a cluster decomposition of the molecular structure
+following the criteria indicated by the options a, b, t and m. This
+process is similar to the approach in "fix shake"_fix_shake.html,
+however, the clusters are not kept contrained. Instead, the position
+is slightly modified only for the computation of long-range forces. A
+good cluster decomposition constitutes in building clusters which
+contain the fastest covalent bonds inside clusters.
+
+If the clusters are chosen suitably, the "run_style
+respa"_run_style.html is stable for outer time-steps of at least 8fs.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about these fixes is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to these fixes.  No global or per-atom quantities are
+stored by these fixes for access by various "output
+commands"_Section_howto.html#howto_15.  No parameter of these fixes
+can be used with the {start/stop} keywords of the "run"_run.html
+command.  These fixes are not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-MISC package. It is only enabled if 
+LAMMPS was built with that package. See the "Making 
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+Currently, it does not support "molecule templates"_molecule.html.
+
+[Related commands:]
+
+
+[Default:] none
+
+:line
+
+:link(Fath2017)
+[(Fath)] Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).

doc/src/fix_gle.txt

@@ -62,7 +62,7 @@ as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
 optimal for a given application and the system of choice can be
 obtained from "(GLE4MD)"_#GLE4MD.
 
-Equilibrium sampling a temperature T is obtained by specifiying the
+Equilibrium sampling a temperature T is obtained by specifying the
 target value as the {Tstart} and {Tstop} arguments, so that the diffusion
 matrix that gives canonical sampling for a given A is computed automatically.
 However, the GLE framework also allow for non-equilibrium sampling, that
@@ -116,7 +116,7 @@ output"_thermo_style.html.
 
 This fix computes a global scalar which can be accessed by various
 "output commands"_Section_howto.html#howto_15.  The scalar is the
-cummulative energy change due to this fix.  The scalar value
+cumulative energy change due to this fix.  The scalar value
 calculated by this fix is "extensive".
 
 [Restrictions:]

doc/src/fix_gravity.txt

@@ -76,7 +76,7 @@ specified as an equal-style "variable"_variable.html.  If the value is
 a variable, it should be specified as v_name, where name is the
 variable name.  In this case, the variable will be evaluated each
 timestep, and its value used to determine the quantity.  You should
-insure that the variable calculates a result in the approriate units,
+insure that the variable calculates a result in the appropriate units,
 e.g. force/mass or degrees.
 
 Equal-style variables can specify formulas with various mathematical

doc/src/fix_halt.txt

@@ -15,15 +15,16 @@ fix ID group-ID halt N attribute operator avalue keyword value ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 halt = style name of this fix command :l
 N = check halt condition every N steps :l
-attribute = hstyle or v_name :l
+attribute = {bondmax} or {tlimit} or v_name :l
-  hstyle = {bondmax}
+  bondmax = length of longest bond in the system
+  tlimit = elapsed CPU time
   v_name = name of "equal-style variable"_variable.html :pre
 operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l
 avalue = numeric value to compare attribute to :l
-string = text string to print with optional variable names :l
 zero or more keyword/value pairs may be appended :l
-keyword = {error} :l
+keyword = {error} or {message} :l
-  {error} value = {hard} or {soft} or {continue} :pre
+  {error} value = {hard} or {soft} or {continue}
+  {message} value = {yes} or {no} :pre
 :ule
 
 [Examples:]
@@ -40,14 +41,33 @@ specified by the "run"_run.html or "minimize"_minimize.html command.
 
 The specified group-ID is ignored by this fix.
 
-The specified {attribute} can be one of the {hstyle} options listed
+The specified {attribute} can be one of the options listed above,
-above, or an "equal-style variable"_variable.html referenced as
+namely {bondmax} or {tlimit}, or an "equal-style
-{v_name}, where "name" is the name of a variable that has been defined
+variable"_variable.html referenced as {v_name}, where "name" is the
-previously in the input script.
+name of a variable that has been defined previously in the input
+script.
 
-The only {hstyle} option currently implemented is {bondmax}.  This
+The {bondmax} attribute will loop over all bonds in the system,
-will loop over all bonds in the system, compute their current
+compute their current lengths, and set {attribute} to the longest bond
-lengths, and set {attribute} to the longest bond distance.
+distance.
+
+The {tlimit} attribute queries the elapsed CPU time (in seconds) since
+the current run began, and sets {attribute} to that value.  This is an
+alternative way to limit the length of a simulation run, similar to
+the "timer"_timer.html timeout command.  There are two differences in
+using this method versus the timer command option.  The first is that
+the clock starts at the beginning of the current run (not when the
+timer or fix command is specified), so that any setup time for the run
+is not included in the elapsed time.  The second is that the timer
+invocation and syncing across all processors (via MPI_Allreduce) is
+not performed once every {N} steps by this command.  Instead it is
+performed (typically) only a small number of times and the elapsed
+times are used to predict when the end-of-the-run will be.  Both of
+these attributes can be useful when performing benchmark calculations
+for a desired length of time with minmimal overhead.  For example, if
+a run is performing 1000s of timesteps/sec, the overhead for syncing
+the timer frequently across a large number of processors may be
+non-negligble.
 
 Equal-style variables evaluate to a numeric value.  See the
 "variable"_variable.html command for a description.  They calculate
@@ -100,6 +120,14 @@ Note that you may wish use the "unfix"_unfix.html command on the fix
 halt ID, so that the same condition is not immediately triggered in a
 subsequent run.
 
+The optional {message} keyword determines whether a message is printed
+to the screen and logfile when the halt condition is triggered.  If
+{message} is set to yes, a one line message with the values that
+triggered the halt is printed.  If {message} is set to no, no message
+is printed; the run simply exits.  The latter may be desirable for
+post-processing tools that extract thermodyanmic information from log
+files.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about this fix is written to "binary restart
@@ -118,4 +146,4 @@ This fix is not invoked during "energy minimization"_minimize.html.
 
 [Default:]
 
-The option defaults are error = hard.
+The option defaults are error = hard and message = yes.

doc/src/fix_indent.txt

@@ -107,7 +107,7 @@ fashion.  For the latter, see the {start} and {stop} keywords of the
 "run"_run.html command and the {elaplong} keyword of "thermo_style
 custom"_thermo_style.html for details.
 
-For example, if a spherical indenter's x-position is specfied as v_x,
+For example, if a spherical indenter's x-position is specified as v_x,
 then this variable definition will keep it's center at a relative
 position in the simulation box, 1/4 of the way from the left edge to
 the right edge, even if the box size changes:
@@ -121,7 +121,7 @@ variable x equal "2.5 + 5*elaplong*dt"
 variable x equal vdisplace(2.5,5) :pre
 
 If a spherical indenter's radius is specified as v_r, then these
-variable definitions will grow the size of the indenter at a specfied
+variable definitions will grow the size of the indenter at a specified
 rate.
 
 variable r0 equal 0.0

doc/src/fix_langevin.txt

@@ -307,7 +307,7 @@ setting the {tally} keyword to {yes}.
 
 This fix computes a global scalar which can be accessed by various
 "output commands"_Section_howto.html#howto_15.  The scalar is the
-cummulative energy change due to this fix.  The scalar value
+cumulative energy change due to this fix.  The scalar value
 calculated by this fix is "extensive".  Note that calculation of this
 quantity requires setting the {tally} keyword to {yes}.