git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7356 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_accelerate.html

@@ -69,7 +69,7 @@ The speed-up due to GPU usage depends on a variety of factors, as
 discussed below.
 </P>
 <P>To see what styles are currently available in each of the accelerated
-packages, see <A HREF = "Section_commands.html#cmd_5">this section</A> of the
+packages, see <A HREF = "Section_commands.html#cmd_5">Section_commands 5</A> of the
 manual.  A list of accelerated styles is included in the pair, fix,
 compute, and kspace sections.
 </P>

doc/Section_accelerate.txt

@@ -66,7 +66,7 @@ The speed-up due to GPU usage depends on a variety of factors, as
 discussed below.
 
 To see what styles are currently available in each of the accelerated
-packages, see "this section"_Section_commands.html#cmd_5 of the
+packages, see "Section_commands 5"_Section_commands.html#cmd_5 of the
 manual.  A list of accelerated styles is included in the pair, fix,
 compute, and kspace sections.
 

doc/Section_howto.html

@@ -674,9 +674,9 @@ of the Python wrapper provided with LAMMPS that operates through the
 LAMMPS library interface.
 </P>
 <P>The files src/library.cpp and library.h contain the C-style interface
-to LAMMPS.  See <A HREF = "Section_howto.html#howto_19">this section</A> of the manual
+to LAMMPS.  See <A HREF = "Section_howto.html#howto_19">Section_howto 19</A> of the
-for a description of the interface and how to extend it for your
+manual for a description of the interface and how to extend it for
-needs.
+your needs.
 </P>
 <P>Note that the lammps_open() function that creates an instance of
 LAMMPS takes an MPI communicator as an argument.  This means that
@@ -1658,10 +1658,10 @@ converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
 
 <A NAME = "howto_19"></A><H4>6.19 Library interface to LAMMPS 
 </H4>
-<P>As described in <A HREF = "Section_start.html#start_4">this section</A>, LAMMPS can
+<P>As described in <A HREF = "Section_start.html#start_4">Section_start 4</A>, LAMMPS
-be built as a library, so that it can be called by another code, used
+can be built as a library, so that it can be called by another code,
-in a <A HREF = "Section_howto.html#howto_10">coupled manner</A> with other codes, or
+used in a <A HREF = "Section_howto.html#howto_10">coupled manner</A> with other
-driven through a <A HREF = "Section_python.html">Python interface</A>.
+codes, or driven through a <A HREF = "Section_python.html">Python interface</A>.
 </P>
 <P>All of these methodologies use a C-style interface to LAMMPS that is
 provided in the files src/library.cpp and src/library.h.  The

doc/Section_howto.txt

@@ -668,9 +668,9 @@ of the Python wrapper provided with LAMMPS that operates through the
 LAMMPS library interface.
 
 The files src/library.cpp and library.h contain the C-style interface
-to LAMMPS.  See "this section"_Section_howto.html#howto_19 of the manual
+to LAMMPS.  See "Section_howto 19"_Section_howto.html#howto_19 of the
-for a description of the interface and how to extend it for your
+manual for a description of the interface and how to extend it for
-needs.
+your needs.
 
 Note that the lammps_open() function that creates an instance of
 LAMMPS takes an MPI communicator as an argument.  This means that
@@ -1645,10 +1645,10 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda
 
 6.19 Library interface to LAMMPS :link(howto_19),h4
 
-As described in "this section"_Section_start.html#start_4, LAMMPS can
+As described in "Section_start 4"_Section_start.html#start_4, LAMMPS
-be built as a library, so that it can be called by another code, used
+can be built as a library, so that it can be called by another code,
-in a "coupled manner"_Section_howto.html#howto_10 with other codes, or
+used in a "coupled manner"_Section_howto.html#howto_10 with other
-driven through a "Python interface"_Section_python.html.
+codes, or driven through a "Python interface"_Section_python.html.
 
 All of these methodologies use a C-style interface to LAMMPS that is
 provided in the files src/library.cpp and src/library.h.  The

doc/Section_intro.html

@@ -51,8 +51,8 @@ LAMMPS performance and scalability, or the Benchmarks section of the
 </P>
 <P>LAMMPS is a freely-available open-source code, distributed under the
 terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A>, which means you can use or
-modify the code however you wish.  See <A HREF = "#intro_4">this section</A> for a brief
+modify the code however you wish.  See <A HREF = "#intro_4">this section</A> for a
-discussion of the open-source philosophy.
+brief discussion of the open-source philosophy.
 </P>
 
 
@@ -421,8 +421,8 @@ Site</A>, or have a suggestion for something to clarify or include,
 send an email to the
 <A HREF = "http://lammps.sandia.gov/authors.html">developers</A>. 
 
-<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">this section</A> describes
+<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">Section_errors 2</A>
-how to report it. 
+describes how to report it. 
 
 <LI>If you publish a paper using LAMMPS results, send the citation (and
 any cool pictures or movies if you like) to add to the Publications,

doc/Section_intro.txt

@@ -47,8 +47,8 @@ LAMMPS performance and scalability, or the Benchmarks section of the
 
 LAMMPS is a freely-available open-source code, distributed under the
 terms of the "GNU Public License"_gnu, which means you can use or
-modify the code however you wish.  See "this section"_#intro_4 for a brief
+modify the code however you wish.  See "this section"_#intro_4 for a
-discussion of the open-source philosophy.
+brief discussion of the open-source philosophy.
 
 :link(gnu,http://www.gnu.org/copyleft/gpl.html)
 
@@ -410,8 +410,8 @@ Site"_lws, or have a suggestion for something to clarify or include,
 send an email to the
 "developers"_http://lammps.sandia.gov/authors.html. :l
 
-If you find a bug, "this section"_Section_errors.html#err_2 describes
+If you find a bug, "Section_errors 2"_Section_errors.html#err_2
-how to report it. :l
+describes how to report it. :l
 
 If you publish a paper using LAMMPS results, send the citation (and
 any cool pictures or movies if you like) to add to the Publications,

doc/Section_packages.html

@@ -25,7 +25,7 @@ molecular systems or granular systems are in packages.  You can see
 the list of all packages by typing "make package" from within the src
 directory of the LAMMPS distribution.
 </P>
-<P>See <A HREF = "Section_start.html#start_3">this section</A> of the manual for
+<P>See <A HREF = "Section_start.html#start_3">Section_start 3</A> of the manual for
 details on how to include/exclude specific packages as part of the
 LAMMPS build process, and for more details about the differences
 between standard packages and user packages in LAMMPS.

doc/Section_packages.txt

@@ -22,7 +22,7 @@ molecular systems or granular systems are in packages.  You can see
 the list of all packages by typing "make package" from within the src
 directory of the LAMMPS distribution.
 
-See "this section"_Section_start.html#start_3 of the manual for
+See "Section_start 3"_Section_start.html#start_3 of the manual for
 details on how to include/exclude specific packages as part of the
 LAMMPS build process, and for more details about the differences
 between standard packages and user packages in LAMMPS.

doc/Section_python.html

@@ -34,8 +34,8 @@ packages.  It can be used to glue multiple pieces of software
 together, e.g. to run a coupled or multiscale model.  See <A HREF = "Section_howto.html#howto_10">this
 section</A> of the manual and the couple
 directory of the distribution for more ideas about coupling LAMMPS to
-other codes.  See <A HREF = "Section_start.html#start_4">this section</A> about how
+other codes.  See <A HREF = "Section_start.html#start_4">Section_start 4</A> about
-to build LAMMPS as a library, and <A HREF = "Section_howto.html#howto_19">this
+how to build LAMMPS as a library, and <A HREF = "Section_howto.html#howto_19">this
 section</A> for a description of the library
 interface provided in src/library.cpp and src/library.h and how to
 extend it for your needs.  As described below, that interface is what
@@ -502,7 +502,7 @@ subscripting.  The one exception is that for a fix that calculates a
 global vector or array, a single double value from the vector or array
 is returned, indexed by I (vector) or I and J (array).  I,J are
 zero-based indices.  The I,J arguments can be left out if not needed.
-See <A HREF = "Section_howto.html#howto_15">this section</A> of the manual for a
+See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> of the manual for a
 discussion of global, per-atom, and local data, and of scalar, vector,
 and array data types.  See the doc pages for individual
 <A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> for a description of what
@@ -582,7 +582,7 @@ following steps:
 src/library.h. 
 
 <LI>Verify the new function is syntactically correct by building LAMMPS as
-a library - see <A HREF = "Section_start.html#start_4">this section</A> of the
+a library - see <A HREF = "Section_start.html#start_4">Section_start 4</A> of the
 manual. 
 
 <LI>Add a wrapper method in the Python LAMMPS module to python/lammps.py

doc/Section_python.txt

@@ -31,8 +31,8 @@ packages.  It can be used to glue multiple pieces of software
 together, e.g. to run a coupled or multiscale model.  See "this
 section"_Section_howto.html#howto_10 of the manual and the couple
 directory of the distribution for more ideas about coupling LAMMPS to
-other codes.  See "this section"_Section_start.html#start_4 about how
+other codes.  See "Section_start 4"_Section_start.html#start_4 about
-to build LAMMPS as a library, and "this
+how to build LAMMPS as a library, and "this
 section"_Section_howto.html#howto_19 for a description of the library
 interface provided in src/library.cpp and src/library.h and how to
 extend it for your needs.  As described below, that interface is what
@@ -497,7 +497,7 @@ subscripting.  The one exception is that for a fix that calculates a
 global vector or array, a single double value from the vector or array
 is returned, indexed by I (vector) or I and J (array).  I,J are
 zero-based indices.  The I,J arguments can be left out if not needed.
-See "this section"_Section_howto.html#howto_15 of the manual for a
+See "Section_howto 15"_Section_howto.html#howto_15 of the manual for a
 discussion of global, per-atom, and local data, and of scalar, vector,
 and array data types.  See the doc pages for individual
 "computes"_compute.html and "fixes"_fix.html for a description of what
@@ -577,7 +577,7 @@ Add a new interface function to src/library.cpp and
 src/library.h. :ulb,l
 
 Verify the new function is syntactically correct by building LAMMPS as
-a library - see "this section"_Section_start.html#start_4 of the
+a library - see "Section_start 4"_Section_start.html#start_4 of the
 manual. :l
 
 Add a wrapper method in the Python LAMMPS module to python/lammps.py

doc/Section_start.html

@@ -717,13 +717,13 @@ src/library.cpp and src/library.h.
 <P>See the sample codes couple/simple/simple.cpp and simple.c as examples
 of C++ and C codes that invoke LAMMPS thru its library interface.
 There are other examples as well in the couple directory which are
-discussed in <A HREF = "Section_howto.html#howto_10">this section</A> of the manual.
+discussed in <A HREF = "Section_howto.html#howto_10">Section_howto 10</A> of the
-See <A HREF = "Section_python.html">Section_python</A> of the manual for a
+manual.  See <A HREF = "Section_python.html">Section_python</A> of the manual for a
 description of the Python wrapper provided with LAMMPS that operates
 through the LAMMPS library interface.
 </P>
 <P>The files src/library.cpp and library.h contain the C-style interface
-to LAMMPS.  See <A HREF = "Section_howto.html#howto_19">this section</A> of the
+to LAMMPS.  See <A HREF = "Section_howto.html#howto_19">Section_howto 19</A> of the
 manual for a description of the interface and how to extend it for
 your needs.
 </P>
@@ -938,9 +938,9 @@ installed on a machine (e.g. your desktop), you can run on more
 (virtual) processors than you have physical processors.
 </P>
 <P>To run multiple independent simulatoins from one input script, using
-multiple partitions, see <A HREF = "Section_howto.html#howto_4">this section</A> of
+multiple partitions, see <A HREF = "Section_howto.html#howto_4">Section_howto 4</A>
-the manual.  World- and universe-style <A HREF = "variable.html">variables</A> are
+of the manual.  World- and universe-style <A HREF = "variable.html">variables</A>
-useful in this context.
+are useful in this context.
 </P>
 <PRE>-plog file 
 </PRE>

doc/Section_start.txt

@@ -711,13 +711,13 @@ src/library.cpp and src/library.h.
 See the sample codes couple/simple/simple.cpp and simple.c as examples
 of C++ and C codes that invoke LAMMPS thru its library interface.
 There are other examples as well in the couple directory which are
-discussed in "this section"_Section_howto.html#howto_10 of the manual.
+discussed in "Section_howto 10"_Section_howto.html#howto_10 of the
-See "Section_python"_Section_python.html of the manual for a
+manual.  See "Section_python"_Section_python.html of the manual for a
 description of the Python wrapper provided with LAMMPS that operates
 through the LAMMPS library interface.
 
 The files src/library.cpp and library.h contain the C-style interface
-to LAMMPS.  See "this section"_Section_howto.html#howto_19 of the
+to LAMMPS.  See "Section_howto 19"_Section_howto.html#howto_19 of the
 manual for a description of the interface and how to extend it for
 your needs.
 
@@ -929,9 +929,9 @@ 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
-multiple partitions, see "this section"_Section_howto.html#howto_4 of
+multiple partitions, see "Section_howto 4"_Section_howto.html#howto_4
-the manual.  World- and universe-style "variables"_variable.html are
+of the manual.  World- and universe-style "variables"_variable.html
-useful in this context.
+are useful in this context.
 
 -plog file :pre
  

doc/compute_ackland_atom.html

@@ -53,8 +53,8 @@ which computes this quantity.-
 </P>
 <P>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
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P><B>Restrictions:</B>
 </P>

doc/compute_ackland_atom.txt

@@ -50,8 +50,8 @@ which computes this quantity.-
 
 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
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 [Restrictions:]
 

doc/compute_centro_atom.html

@@ -79,8 +79,8 @@ too frequently or to have multiple compute/dump commands, each with a
 </P>
 <P>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
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values are unitless values >= 0.0.  Their
 magnitude depends on the lattice style due to the number of

doc/compute_centro_atom.txt

@@ -75,8 +75,8 @@ too frequently or to have multiple compute/dump commands, each with a
 
 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
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values are unitless values >= 0.0.  Their
 magnitude depends on the lattice style due to the number of

doc/compute_cluster_atom.html

@@ -46,8 +46,8 @@ too frequently or to have multiple compute/dump commands, each of a
 </P>
 <P>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
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values will be an ID > 0, as explained above.
 </P>

doc/compute_cluster_atom.txt

@@ -43,8 +43,8 @@ too frequently or to have multiple compute/dump commands, each of a
 
 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
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values will be an ID > 0, as explained above.
 

doc/compute_cna_atom.html

@@ -77,8 +77,8 @@ too frequently or to have multiple compute/dump commands, each with a
 </P>
 <P>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
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values will be a number from 0 to 5, as explained
 above.

doc/compute_cna_atom.txt

@@ -74,8 +74,8 @@ too frequently or to have multiple compute/dump commands, each with a
 
 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
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values will be a number from 0 to 5, as explained
 above.

doc/compute_com_molecule.html

@@ -64,8 +64,8 @@ file</A> containing coordinates of the atoms in the bodies.
 Nmolecules and the number of columns = 3 for the x,y,z center-of-mass
 coordinates of each molecule.  These values can be accessed by any
 command that uses global array values from a compute as input.  See
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The array values are "intensive".  The array values will be in
 distance <A HREF = "units.html">units</A>.

doc/compute_com_molecule.txt

@@ -61,8 +61,8 @@ This compute calculates a global array where the number of rows =
 Nmolecules and the number of columns = 3 for the x,y,z center-of-mass
 coordinates of each molecule.  These values can be accessed by any
 command that uses global array values from a compute as input.  See
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The array values are "intensive".  The array values will be in
 distance "units"_units.html.

doc/compute_coord_atom.html

@@ -46,8 +46,8 @@ too frequently or to have multiple compute/dump commands, each of a
 </P>
 <P>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
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values will be a number >= 0.0, as explained
 above.

doc/compute_coord_atom.txt

@@ -43,8 +43,8 @@ too frequently or to have multiple compute/dump commands, each of a
 
 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
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values will be a number >= 0.0, as explained
 above.

doc/compute_damage_atom.html

@@ -37,8 +37,8 @@ compute group.
 </P>
 <P>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
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values will be a number >= 0.0, as explained
 above.

doc/compute_damage_atom.txt

@@ -34,8 +34,8 @@ compute group.
 
 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
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values will be a number >= 0.0, as explained
 above.

doc/compute_displace_atom.html

@@ -76,8 +76,9 @@ file.
 </P>
 <P>This compute calculates a per-atom array with 4 columns, which can be
 accessed by indices 1-4 by any command that uses per-atom values from
-a compute as input.  See <A HREF = "Section_howto.html#howto_15">this section</A>
+a compute as input.  See <A HREF = "Section_howto.html#howto_15">Section_howto
-for an overview of LAMMPS output options.
+15</A> for an overview of LAMMPS output
+options.
 </P>
 <P>The per-atom array values will be in distance <A HREF = "units.html">units</A>.
 </P>

doc/compute_displace_atom.txt

@@ -73,8 +73,9 @@ file.
 
 This compute calculates a per-atom array with 4 columns, which can be
 accessed by indices 1-4 by any command that uses per-atom values from
-a compute as input.  See "this section"_Section_howto.html#howto_15
+a compute as input.  See "Section_howto
-for an overview of LAMMPS output options.
+15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+options.
 
 The per-atom array values will be in distance "units"_units.html.
 

doc/compute_erotate_asphere.html

@@ -43,8 +43,8 @@ inertia will be the same as in 3d.
 </P>
 <P>This compute calculates a global scalar (the KE).  This value can be
 used by any command that uses a global scalar value from a compute as
-input.  See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
+input.  See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 </P>
 <P>The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy <A HREF = "units.html">units</A>.

doc/compute_erotate_asphere.txt

@@ -40,8 +40,8 @@ inertia will be the same as in 3d.
 
 This compute calculates a global scalar (the KE).  This value can be
 used by any command that uses a global scalar value from a compute as
-input.  See "this section"_Section_howto.html#howto_15 for an overview
+input.  See "Section_howto 15"_Section_howto.html#howto_15 for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 
 The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy "units"_units.html.

doc/compute_erotate_sphere.html

@@ -38,8 +38,8 @@ same as in 3d.
 </P>
 <P>This compute calculates a global scalar (the KE).  This value can be
 used by any command that uses a global scalar value from a compute as
-input.  See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
+input.  See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 </P>
 <P>The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy <A HREF = "units.html">units</A>.

doc/compute_erotate_sphere.txt

@@ -35,8 +35,8 @@ same as in 3d.
 
 This compute calculates a global scalar (the KE).  This value can be
 used by any command that uses a global scalar value from a compute as
-input.  See "this section"_Section_howto.html#howto_15 for an overview
+input.  See "Section_howto 15"_Section_howto.html#howto_15 for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 
 The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy "units"_units.html.

doc/compute_event_displace.html

@@ -46,8 +46,8 @@ local atom displacements and may generate "false postives."
 </P>
 <P>This compute calculates a global scalar (the flag).  This value can be
 used by any command that uses a global scalar value from a compute as
-input.  See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
+input.  See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 </P>
 <P>The scalar value calculated by this compute is "intensive".  The
 scalar value will be a 0 or 1 as explained above.

doc/compute_event_displace.txt

@@ -43,8 +43,8 @@ local atom displacements and may generate "false postives."
 
 This compute calculates a global scalar (the flag).  This value can be
 used by any command that uses a global scalar value from a compute as
-input.  See "this section"_Section_howto.html#howto_15 for an overview
+input.  See "Section_howto 15"_Section_howto.html#howto_15 for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 
 The scalar value calculated by this compute is "intensive".  The
 scalar value will be a 0 or 1 as explained above.

doc/compute_gyration.html

@@ -49,8 +49,8 @@ image</A> command.
 </P>
 <P>This compute calculates a global scalar (Rg).  This value can be used
 by any command that uses a global scalar value from a compute as
-input.  See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
+input.  See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 </P>
 <P>The scalar value calculated by this compute is "intensive".  The
 scalar value will be in distance <A HREF = "units.html">units</A>.

doc/compute_gyration.txt

@@ -46,8 +46,8 @@ image"_set.html command.
 
 This compute calculates a global scalar (Rg).  This value can be used
 by any command that uses a global scalar value from a compute as
-input.  See "this section"_Section_howto.html#howto_15 for an overview
+input.  See "Section_howto 15"_Section_howto.html#howto_15 for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 
 The scalar value calculated by this compute is "intensive".  The
 scalar value will be in distance "units"_units.html.

doc/compute_ke.html

@@ -47,8 +47,8 @@ include different degrees of freedom (translational, rotational, etc).
 </P>
 <P>This compute calculates a global scalar (the KE).  This value can be
 used by any command that uses a global scalar value from a compute as
-input.  See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
+input.  See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 </P>
 <P>The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy <A HREF = "units.html">units</A>.

doc/compute_ke.txt

@@ -44,8 +44,8 @@ include different degrees of freedom (translational, rotational, etc).
 
 This compute calculates a global scalar (the KE).  This value can be
 used by any command that uses a global scalar value from a compute as
-input.  See "this section"_Section_howto.html#howto_15 for an overview
+input.  See "Section_howto 15"_Section_howto.html#howto_15 for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 
 The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy "units"_units.html.

doc/compute_ke_atom.html

@@ -37,8 +37,8 @@ specified compute group.
 </P>
 <P>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
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
 </P>

doc/compute_ke_atom.txt

@@ -34,8 +34,8 @@ specified compute group.
 
 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
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values will be in energy "units"_units.html.
 

doc/compute_ke_atom_eff.html

@@ -62,8 +62,8 @@ electrons) not in the specified compute group.
 </P>
 <P>This compute calculates a scalar quantity for each atom, which can be
 accessed by any command that uses per-atom computes as input.  See
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
 </P>

doc/compute_ke_atom_eff.txt

@@ -59,8 +59,8 @@ electrons) not in the specified compute group.
 
 This compute calculates a scalar quantity for each atom, which can be
 accessed by any command that uses per-atom computes as input.  See
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values will be in energy "units"_units.html.
 

doc/compute_ke_eff.html

@@ -64,8 +64,8 @@ thermo_modify   temp effTemp
 </P>
 <P>This compute calculates a global scalar (the KE).  This value can be
 used by any command that uses a global scalar value from a compute as
-input.  See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
+input.  See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 </P>
 <P>The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy <A HREF = "units.html">units</A>.

doc/compute_ke_eff.txt

@@ -61,8 +61,8 @@ See "compute temp/eff"_compute_temp_eff.html.
 
 This compute calculates a global scalar (the KE).  This value can be
 used by any command that uses a global scalar value from a compute as
-input.  See "this section"_Section_howto.html#howto_15 for an overview
+input.  See "Section_howto 15"_Section_howto.html#howto_15 for an
-of LAMMPS output options.
+overview of LAMMPS output options.
 
 The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy "units"_units.html.

doc/compute_meso_e_atom.html

@@ -41,8 +41,8 @@ specified compute group.
 </P>
 <P>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
-<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
 </P>

doc/compute_meso_e_atom.txt

@@ -38,8 +38,8 @@ specified compute group.
 
 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
-"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values will be in energy "units"_units.html.
 

doc/compute_meso_rho_atom.html

@@ -41,8 +41,8 @@ specified compute group.
 </P>
 <P>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
-<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values will be in mass/volume <A HREF = "units.html">units</A>.
 </P>

doc/compute_meso_rho_atom.txt

@@ -38,8 +38,8 @@ specified compute group.
 
 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
-"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values will be in mass/volume "units"_units.html.
 

doc/compute_meso_t_atom.html

@@ -43,8 +43,8 @@ specified compute group.
 </P>
 <P>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
-<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values will be in temperature <A HREF = "units.html">units</A>.
 </P>

doc/compute_meso_t_atom.txt

@@ -40,8 +40,8 @@ specified compute group.
 
 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
-"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values will be in temperature "units"_units.html.
 

doc/compute_pe.html

@@ -83,8 +83,9 @@ more instructions on how to use the accelerated styles effectively.
 </P>
 <P>This compute calculates a global scalar (the potential energy).  This
 value can be used by any command that uses a global scalar value from
-a compute as input.  See <A HREF = "Section_howto.html#howto_15">this section</A>
+a compute as input.  See <A HREF = "Section_howto.html#howto_15">Section_howto
-for an overview of LAMMPS output options.
+15</A> for an overview of LAMMPS output
+options.
 </P>
 <P>The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy <A HREF = "units.html">units</A>.

doc/compute_pe.txt

@@ -79,8 +79,9 @@ more instructions on how to use the accelerated styles effectively.
 
 This compute calculates a global scalar (the potential energy).  This
 value can be used by any command that uses a global scalar value from
-a compute as input.  See "this section"_Section_howto.html#howto_15
+a compute as input.  See "Section_howto
-for an overview of LAMMPS output options.
+15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+options.
 
 The scalar value calculated by this compute is "extensive".  The
 scalar value will be in energy "units"_units.html.

doc/compute_pe_atom.html

@@ -70,8 +70,8 @@ the system energy.
 </P>
 <P>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
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
 </P>

doc/compute_pe_atom.txt

@@ -67,8 +67,8 @@ the system energy.
 
 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
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The per-atom vector values will be in energy "units"_units.html.
 

doc/compute_rdf.html

@@ -104,8 +104,8 @@ coordinate (center of the bin), Each successive set of 2 columns has
 the g(r) and coord(r) values for a specific set of <I>itypeN</I> versus
 <I>jtypeN</I> interactions, as described above.  These values can be used
 by any command that uses a global values from a compute as input.  See
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
-output options.
+LAMMPS output options.
 </P>
 <P>The array values calculated by this compute are all "intensive".
 </P>

doc/compute_rdf.txt

@@ -101,8 +101,8 @@ coordinate (center of the bin), Each successive set of 2 columns has
 the g(r) and coord(r) values for a specific set of {itypeN} versus
 {jtypeN} interactions, as described above.  These values can be used
 by any command that uses a global values from a compute as input.  See
-"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+"Section_howto 15"_Section_howto.html#howto_15 for an overview of
-output options.
+LAMMPS output options.
 
 The array values calculated by this compute are all "intensive".
 

doc/compute_reduce.html

@@ -173,8 +173,8 @@ divides by the appropriate atom count.
 specified or a global vector of length N where N is the number of
 inputs, and which can be accessed by indices 1 to N.  These values can
 be used by any command that uses global scalar or vector values from a
-compute as input.  See <A HREF = "Section_howto.html#howto_15">this section</A> for
+compute as input.  See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A>
-an overview of LAMMPS output options.
+for an overview of LAMMPS output options.
 </P>
 <P>All the scalar or vector values calculated by this compute are
 "intensive", except when the <I>sum</I> mode is used on per-atom or local

doc/compute_reduce.txt

@@ -160,8 +160,8 @@ This compute calculates a global scalar if a single input value is
 specified or a global vector of length N where N is the number of
 inputs, and which can be accessed by indices 1 to N.  These values can
 be used by any command that uses global scalar or vector values from a
-compute as input.  See "this section"_Section_howto.html#howto_15 for
+compute as input.  See "Section_howto 15"_Section_howto.html#howto_15
-an overview of LAMMPS output options.
+for an overview of LAMMPS output options.
 
 All the scalar or vector values calculated by this compute are
 "intensive", except when the {sum} mode is used on per-atom or local

doc/compute_stress_atom.html

@@ -102,8 +102,9 @@ contribution can easily be computed.
 </P>
 <P>This compute calculates a per-atom array with 6 columns, which can be
 accessed by indices 1-6 by any command that uses per-atom values from
-a compute as input.  See <A HREF = "Section_howto.html#howto_15">this section</A>
+a compute as input.  See <A HREF = "Section_howto.html#howto_15">Section_howto
-for an overview of LAMMPS output options.
+15</A> for an overview of LAMMPS output
+options.
 </P>
 <P>The per-atom array values will be in pressure*volume
 <A HREF = "units.html">units</A> as discussed above.

doc/compute_stress_atom.txt

@@ -99,8 +99,9 @@ contribution can easily be computed.
 
 This compute calculates a per-atom array with 6 columns, which can be
 accessed by indices 1-6 by any command that uses per-atom values from
-a compute as input.  See "this section"_Section_howto.html#howto_15
+a compute as input.  See "Section_howto
-for an overview of LAMMPS output options.
+15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+options.
 
 The per-atom array values will be in pressure*volume
 "units"_units.html as discussed above.

doc/compute_ti.html

@@ -102,8 +102,9 @@ du/dl can be found in the paper by <A HREF = "#Eike">Eike</A>.
 </P>
 <P>This compute calculates a global scalar, namely dUs/dlambda.  This
 value can be used by any command that uses a global scalar value from
-a compute as input.  See <A HREF = "Section_howto.html#howto_15">this section</A>
+a compute as input.  See <A HREF = "Section_howto.html#howto_15">Section_howto
-for an overview of LAMMPS output options.
+15</A> for an overview of LAMMPS output
+options.
 </P>
 <P>The scalar value calculated by this compute is "extensive".
 </P>

doc/compute_ti.txt

@@ -94,8 +94,9 @@ du/dl can be found in the paper by "Eike"_#Eike.
 
 This compute calculates a global scalar, namely dUs/dlambda.  This
 value can be used by any command that uses a global scalar value from
-a compute as input.  See "this section"_Section_howto.html#howto_15
+a compute as input.  See "Section_howto
-for an overview of LAMMPS output options.
+15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+options.
 
 The scalar value calculated by this compute is "extensive".
 

doc/create_box.html

@@ -55,9 +55,9 @@ since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
 geometrically equivalent.
 </P>
-<P>See <A HREF = "Section_howto.html#howto_12">this section</A> of the doc pages for a
+<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
-geometric description of triclinic boxes, as defined by LAMMPS, and
+for a geometric description of triclinic boxes, as defined by LAMMPS,
-how to transform these parameters to and from other commonly used
+and how to transform these parameters to and from other commonly used
 triclinic representations.
 </P>
 <P>When a prism region is used, the simulation domain must be periodic in

doc/create_box.txt

@@ -52,9 +52,9 @@ since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
 geometrically equivalent.
 
-See "this section"_Section_howto.html#howto_12 of the doc pages for a
+See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
-geometric description of triclinic boxes, as defined by LAMMPS, and
+for a geometric description of triclinic boxes, as defined by LAMMPS,
-how to transform these parameters to and from other commonly used
+and how to transform these parameters to and from other commonly used
 triclinic representations.
 
 When a prism region is used, the simulation domain must be periodic in

doc/dump.html

@@ -283,9 +283,9 @@ coordinate format that many codes can read.
 </P>
 <P>Note that DCD, XTC, and XYZ formatted files can be read directly by
 <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> (a popular molecular viewing
-program).  See <A HREF = "Section_tools.html#vmd">this section</A> of the manual and
+program).  See <A HREF = "Section_tools.html#vmd">Section tools</A> of the manual
-the tools/lmp2vmd/README.txt file for more information about support
+and the tools/lmp2vmd/README.txt file for more information about
-in VMD for reading and visualizing LAMMPS dump files.
+support in VMD for reading and visualizing LAMMPS dump files.
 </P>
 <HR>
 

doc/dump.txt

@@ -272,9 +272,9 @@ coordinate format that many codes can read.
 
 Note that DCD, XTC, and XYZ formatted files can be read directly by
 "VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular molecular viewing
-program).  See "this section"_Section_tools.html#vmd of the manual and
+program).  See "Section tools"_Section_tools.html#vmd of the manual
-the tools/lmp2vmd/README.txt file for more information about support
+and the tools/lmp2vmd/README.txt file for more information about
-in VMD for reading and visualizing LAMMPS dump files.
+support in VMD for reading and visualizing LAMMPS dump files.
 
 :line
 

doc/fix_append_atoms.html

@@ -87,9 +87,9 @@ define the lattice spacings.
 <P>No information about this fix is written to <A HREF = "restart.html">binary restart
 files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
 are relevant to this fix.  No global or per-atom quantities are stored
-by this fix for access by various <A HREF = "Section_howto.html#4_15">output
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
-commands</A>.  No parameter of this fix can be
+commands</A>.  No parameter of this fix can
-used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
 This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>
@@ -98,8 +98,9 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
 LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
 LAMMPS</A> section for more info.
 </P>
-<P>The zhi boundary on which atoms are added with append_atoms must be shrink-wrapped.
+<P>The zhi boundary on which atoms are added with append_atoms must be
-The zlo boundary may be any boundary type other than periodic.
+shrink-wrapped.  The zlo boundary may be any boundary type other than
+periodic.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/fix_append_atoms.txt

@@ -78,8 +78,8 @@ No information about this fix is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various "output
-commands"_Section_howto.html#4_15.  No parameter of this fix can be
+commands"_Section_howto.html#howto_15.  No parameter of this fix can
-used with the {start/stop} keywords of the "run"_run.html command.
+be used with the {start/stop} keywords of the "run"_run.html command.
 This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]
@@ -88,8 +88,9 @@ This fix style is part of the SHOCK 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 zhi boundary on which atoms are added with append_atoms must be shrink-wrapped.
+The zhi boundary on which atoms are added with append_atoms must be
-The zlo boundary may be any boundary type other than periodic.
+shrink-wrapped.  The zlo boundary may be any boundary type other than
+periodic.
 
 [Related commands:]
 

doc/fix_meso.html

@@ -37,9 +37,9 @@ LAMMPS.
 <P>No information about this fix is written to <A HREF = "restart.html">binary restart
 files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
 are relevant to this fix.  No global or per-atom quantities are stored
-by this fix for access by various <A HREF = "Section_howto.html#4_15">output
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
-commands</A>.  No parameter of this fix can be
+commands</A>.  No parameter of this fix can
-used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
 This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>

doc/fix_meso.txt

@@ -35,8 +35,8 @@ No information about this fix is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various "output
-commands"_Section_howto.html#4_15.  No parameter of this fix can be
+commands"_Section_howto.html#howto_15.  No parameter of this fix can
-used with the {start/stop} keywords of the "run"_run.html command.
+be used with the {start/stop} keywords of the "run"_run.html command.
 This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]

doc/fix_meso_stationary.html

@@ -38,9 +38,9 @@ LAMMPS.
 <P>No information about this fix is written to <A HREF = "restart.html">binary restart
 files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
 are relevant to this fix.  No global or per-atom quantities are stored
-by this fix for access by various <A HREF = "Section_howto.html#4_15">output
+by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
-commands</A>.  No parameter of this fix can be
+commands</A>.  No parameter of this fix can
-used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
 This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>

doc/fix_meso_stationary.txt

@@ -36,8 +36,8 @@ No information about this fix is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various "output
-commands"_Section_howto.html#4_15.  No parameter of this fix can be
+commands"_Section_howto.html#howto_15.  No parameter of this fix can
-used with the {start/stop} keywords of the "run"_run.html command.
+be used with the {start/stop} keywords of the "run"_run.html command.
 This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]

doc/fix_neb.html

@@ -29,8 +29,8 @@
 simulation run via the <A HREF = "neb.html">neb</A> command to perform a nudged
 elastic band (NEB) calculation for transition state finding.  Hi-level
 explanations of NEB are given with the <A HREF = "neb.html">neb</A> command and in
-<A HREF = "Section_howto.html#howto_5">this section</A> of the manual.  The fix neb
+<A HREF = "Section_howto.html#howto_5">Section_howto 5</A> of the manual.  The fix
-command must be used with the "neb" command to define how
+neb command must be used with the "neb" command to define how
 inter-replica forces are computed.
 </P>
 <P>Only the N atoms in the fix group experience inter-replica forces.

doc/fix_neb.txt

@@ -26,8 +26,8 @@ Add inter-replica forces to atoms in the group for a multi-replica
 simulation run via the "neb"_neb.html command to perform a nudged
 elastic band (NEB) calculation for transition state finding.  Hi-level
 explanations of NEB are given with the "neb"_neb.html command and in
-"this section"_Section_howto.html#howto_5 of the manual.  The fix neb
+"Section_howto 5"_Section_howto.html#howto_5 of the manual.  The fix
-command must be used with the "neb" command to define how
+neb command must be used with the "neb" command to define how
 inter-replica forces are computed.
 
 Only the N atoms in the fix group experience inter-replica forces.

doc/fix_viscosity.html

@@ -103,12 +103,13 @@ you cannot accurately infer a viscosity and should try increasing
 the Nevery parameter.
 </P>
 <P>An alternative method for calculating a viscosity is to run a NEMD
-simulation, as described in <A HREF = "Section_howto.html#howto_13">this section</A>
+simulation, as described in <A HREF = "Section_howto.html#howto_13">Section_howto
-of the manual.  NEMD simulations deform the simmulation box via the
+13</A> of the manual.  NEMD simulations
-<A HREF = "fix_deform.html">fix deform</A> command.  Thus they cannot be run on a
+deform the simmulation box via the <A HREF = "fix_deform.html">fix deform</A>
-charged system using a <A HREF = "kspace_style.html">PPPM solver</A> since PPPM does
+command.  Thus they cannot be run on a charged system using a <A HREF = "kspace_style.html">PPPM
-not currently support non-orthogonal boxes.  Using fix viscosity keeps
+solver</A> since PPPM does not currently support
-the box orthogonal; thus it does not suffer from this limitation.
+non-orthogonal boxes.  Using fix viscosity keeps the box orthogonal;
+thus it does not suffer from this limitation.
 </P>
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>

doc/fix_viscosity.txt

@@ -92,12 +92,13 @@ you cannot accurately infer a viscosity and should try increasing
 the Nevery parameter.
 
 An alternative method for calculating a viscosity is to run a NEMD
-simulation, as described in "this section"_Section_howto.html#howto_13
+simulation, as described in "Section_howto
-of the manual.  NEMD simulations deform the simmulation box via the
+13"_Section_howto.html#howto_13 of the manual.  NEMD simulations
-"fix deform"_fix_deform.html command.  Thus they cannot be run on a
+deform the simmulation box via the "fix deform"_fix_deform.html
-charged system using a "PPPM solver"_kspace_style.html since PPPM does
+command.  Thus they cannot be run on a charged system using a "PPPM
-not currently support non-orthogonal boxes.  Using fix viscosity keeps
+solver"_kspace_style.html since PPPM does not currently support
-the box orthogonal; thus it does not suffer from this limitation.
+non-orthogonal boxes.  Using fix viscosity keeps the box orthogonal;
+thus it does not suffer from this limitation.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 

doc/fix_wall_piston.html

@@ -101,9 +101,9 @@ define the lattice spacings.
 <P>No information about this fix is written to <A HREF = "restart.html">binary restart
 files</A>.  None of the <A HREF = "fix_modify.html">fix_modify</A> options
 are relevant to this fix.  No global or per-atom quantities are stored
-by this fix for access by various <A HREF = "Section_howto.html#4_15">output
+by this fix for access by various <A HREF = "Section_howto.html#howoto_15">output
-commands</A>.  No parameter of this fix can be
+commands</A>.  No parameter of this fix can
-used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
 This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
 <P><B>Restrictions:</B>

doc/fix_wall_piston.txt

@@ -92,8 +92,8 @@ No information about this fix is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various "output
-commands"_Section_howto.html#4_15.  No parameter of this fix can be
+commands"_Section_howto.html#howoto_15.  No parameter of this fix can
-used with the {start/stop} keywords of the "run"_run.html command.
+be used with the {start/stop} keywords of the "run"_run.html command.
 This fix is not invoked during "energy minimization"_minimize.html.
 
 [Restrictions:]

doc/if.html

@@ -66,9 +66,9 @@ above.
 <P>IMPORTANT NOTE: If a command itself requires a quoted argument (e.g. a
 <A HREF = "print.html">print</A> command), then double and single quotes can be used
 and nested in the usual manner, as in the examples above and below.
-See <A HREF = "Section_commands.html#cmd_2">this section</A> of the manual for more
+See <A HREF = "Section_commands.html#cmd_2">Section_commands 2</A> of the manual for
-details on using quotes in arguments.  Only one of level of nesting is
+more details on using quotes in arguments.  Only one of level of
-allowed, but that should be sufficient for most use cases.
+nesting is allowed, but that should be sufficient for most use cases.
 </P>
 <P>Note that by using the line continuation character "&", the if command
 can be spread across many lines, though it is still a single command:

doc/if.txt

@@ -63,9 +63,9 @@ above.
 IMPORTANT NOTE: If a command itself requires a quoted argument (e.g. a
 "print"_print.html command), then double and single quotes can be used
 and nested in the usual manner, as in the examples above and below.
-See "this section"_Section_commands.html#cmd_2 of the manual for more
+See "Section_commands 2"_Section_commands.html#cmd_2 of the manual for
-details on using quotes in arguments.  Only one of level of nesting is
+more details on using quotes in arguments.  Only one of level of
-allowed, but that should be sufficient for most use cases.
+nesting is allowed, but that should be sufficient for most use cases.
 
 Note that by using the line continuation character "&", the if command
 can be spread across many lines, though it is still a single command:

doc/log.html

@@ -33,7 +33,7 @@ the same log file.
 </P>
 <P>The file "log.lammps" is the default log file for a LAMMPS run.  The
 name of the initial log file can also be set by the command-line
-switch -log.  See <A HREF = "Section_start.html#start_6">this section</A> for
+switch -log.  See <A HREF = "Section_start.html#start_6">Section_start 6</A> for
 details.
 </P>
 <P><B>Restrictions:</B> none

doc/log.txt

@@ -30,7 +30,7 @@ the same log file.
 
 The file "log.lammps" is the default log file for a LAMMPS run.  The
 name of the initial log file can also be set by the command-line
-switch -log.  See "this section"_Section_start.html#start_6 for
+switch -log.  See "Section_start 6"_Section_start.html#start_6 for
 details.
 
 [Restrictions:] none

doc/neb.html

@@ -42,11 +42,11 @@ follows the discussion in these 3 papers: <A HREF = "#Henkelman1">(Henkelman1)</
 </P>
 <P>Each replica runs on a partition of one or more processors.  Processor
 partitions are defined at run-time using the -partition command-line
-switch; see <A HREF = "Section_start.html#start_6">this section</A> of the manual.
+switch; see <A HREF = "Section_start.html#start_6">Section_start 6</A> of the
-Note that if you have MPI installed, you can run a multi-replica
+manual.  Note that if you have MPI installed, you can run a
-simulation with more replicas (partitions) than you have physical
+multi-replica simulation with more replicas (partitions) than you have
-processors, e.g you can run a 10-replica simulation on one or two
+physical processors, e.g you can run a 10-replica simulation on one or
-processors.  You will simply not get the performance speed-up you
+two processors.  You will simply not get the performance speed-up you
 would see with one or more physical processors per replica.  See <A HREF = "Section_howto.html#howto_5">this
 section</A> of the manual for further
 discussion.

doc/neb.txt

@@ -39,11 +39,11 @@ follows the discussion in these 3 papers: "(Henkelman1)"_#Henkelman1,
 
 Each replica runs on a partition of one or more processors.  Processor
 partitions are defined at run-time using the -partition command-line
-switch; see "this section"_Section_start.html#start_6 of the manual.
+switch; see "Section_start 6"_Section_start.html#start_6 of the
-Note that if you have MPI installed, you can run a multi-replica
+manual.  Note that if you have MPI installed, you can run a
-simulation with more replicas (partitions) than you have physical
+multi-replica simulation with more replicas (partitions) than you have
-processors, e.g you can run a 10-replica simulation on one or two
+physical processors, e.g you can run a 10-replica simulation on one or
-processors.  You will simply not get the performance speed-up you
+two processors.  You will simply not get the performance speed-up you
 would see with one or more physical processors per replica.  See "this
 section"_Section_howto.html#howto_5 of the manual for further
 discussion.

doc/partition.html

@@ -30,7 +30,7 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1
 </P>
 <P>This command invokes the specified command on a subset of the
 partitions of processors you have defined via the -partition
-command-line switch.  See <A HREF = "Section_start.html#start_6">this section</A>
+command-line switch.  See <A HREF = "Section_start.html#start_6">Section_start 6</A>
 for an explanation of the switch.
 </P>
 <P>Normally, every input script command in your script is invoked by

doc/partition.txt

@@ -27,7 +27,7 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre
 
 This command invokes the specified command on a subset of the
 partitions of processors you have defined via the -partition
-command-line switch.  See "this section"_Section_start.html#start_6
+command-line switch.  See "Section_start 6"_Section_start.html#start_6
 for an explanation of the switch.
 
 Normally, every input script command in your script is invoked by

doc/prd.html

@@ -71,13 +71,13 @@ event to occur.
 </P>
 <P>Each replica runs on a partition of one or more processors.  Processor
 partitions are defined at run-time using the -partition command-line
-switch; see <A HREF = "Section_start.html#start_6">this section</A> of the manual.
+switch; see <A HREF = "Section_start.html#start_6">Section_start 6</A> of the
-Note that if you have MPI installed, you can run a multi-replica
+manual.  Note that if you have MPI installed, you can run a
-simulation with more replicas (partitions) than you have physical
+multi-replica simulation with more replicas (partitions) than you have
-processors, e.g you can run a 10-replica simulation on one or two
+physical processors, e.g you can run a 10-replica simulation on one or
-processors.  For PRD, this makes little sense, since this offers no
+two processors.  For PRD, this makes little sense, since this offers
-effective parallel speed-up in searching for infrequent events. See
+no effective parallel speed-up in searching for infrequent events. See
-<A HREF = "Section_howto.html#howto_5">this section</A> of the manual for further
+<A HREF = "Section_howto.html#howto_5">Section_howto 5</A> of the manual for further
 discussion.
 </P>
 <P>When a PRD simulation is performed, it is assumed that each replica is

doc/prd.txt

@@ -58,13 +58,13 @@ event to occur.
 
 Each replica runs on a partition of one or more processors.  Processor
 partitions are defined at run-time using the -partition command-line
-switch; see "this section"_Section_start.html#start_6 of the manual.
+switch; see "Section_start 6"_Section_start.html#start_6 of the
-Note that if you have MPI installed, you can run a multi-replica
+manual.  Note that if you have MPI installed, you can run a
-simulation with more replicas (partitions) than you have physical
+multi-replica simulation with more replicas (partitions) than you have
-processors, e.g you can run a 10-replica simulation on one or two
+physical processors, e.g you can run a 10-replica simulation on one or
-processors.  For PRD, this makes little sense, since this offers no
+two processors.  For PRD, this makes little sense, since this offers
-effective parallel speed-up in searching for infrequent events. See
+no effective parallel speed-up in searching for infrequent events. See
-"this section"_Section_howto.html#howto_5 of the manual for further
+"Section_howto 5"_Section_howto.html#howto_5 of the manual for further
 discussion.
 
 When a PRD simulation is performed, it is assumed that each replica is

doc/read_data.html

@@ -111,9 +111,9 @@ limitation, since if the maximum tilt factor is 5 (as in this
 example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
 ... are all geometrically equivalent.
 </P>
-<P>See <A HREF = "Section_howto.html#howto_12">this section</A> of the doc pages for a
+<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
-geometric description of triclinic boxes, as defined by LAMMPS, and
+for a geometric description of triclinic boxes, as defined by LAMMPS,
-how to transform these parameters to and from other commonly used
+and how to transform these parameters to and from other commonly used
 triclinic representations.
 </P>
 <P>When a triclinic system is used, the simulation domain must be

doc/read_data.txt

@@ -108,9 +108,9 @@ limitation, since if the maximum tilt factor is 5 (as in this
 example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
 ... are all geometrically equivalent.
 
-See "this section"_Section_howto.html#howto_12 of the doc pages for a
+See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
-geometric description of triclinic boxes, as defined by LAMMPS, and
+for a geometric description of triclinic boxes, as defined by LAMMPS,
-how to transform these parameters to and from other commonly used
+and how to transform these parameters to and from other commonly used
 triclinic representations.
 
 When a triclinic system is used, the simulation domain must be

doc/region.html

@@ -175,9 +175,9 @@ since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
 geometrically equivalent.
 </P>
-<P>See <A HREF = "Section_howto.html#howto_12">this section</A> of the doc pages for a
+<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
-geometric description of triclinic boxes, as defined by LAMMPS, and
+for a geometric description of triclinic boxes, as defined by LAMMPS,
-how to transform these parameters to and from other commonly used
+and how to transform these parameters to and from other commonly used
 triclinic representations.
 </P>
 <P>The <I>union</I> style creates a region consisting of the volume of all the

doc/region.txt

@@ -166,9 +166,9 @@ since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
 geometrically equivalent.
 
-See "this section"_Section_howto.html#howto_12 of the doc pages for a
+See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
-geometric description of triclinic boxes, as defined by LAMMPS, and
+for a geometric description of triclinic boxes, as defined by LAMMPS,
-how to transform these parameters to and from other commonly used
+and how to transform these parameters to and from other commonly used
 triclinic representations.
 
 The {union} style creates a region consisting of the volume of all the

doc/run_style.html

@@ -69,7 +69,7 @@ simulations performed by LAMMPS.
 
 <P>The <I>verlet/split</I> style is also a velocity-Verlet integrator, but it
 splits the force calculation within each timestep over 2 partitions of
-processors.  See <A HREF = "Section_start.html#start_6">this section</A> for an
+processors.  See <A HREF = "Section_start.html#start_6">Section_start 6</A> for an
 explanation of the -partition command-line switch.
 </P>
 <P>Specifically, this style performs all computation except the

doc/run_style.txt

@@ -64,7 +64,7 @@ The {verlet} style is a standard velocity-Verlet integrator.
 
 The {verlet/split} style is also a velocity-Verlet integrator, but it
 splits the force calculation within each timestep over 2 partitions of
-processors.  See "this section"_Section_start.html#start_6 for an
+processors.  See "Section_start 6"_Section_start.html#start_6 for an
 explanation of the -partition command-line switch.
 
 Specifically, this style performs all computation except the

doc/tad.html

@@ -102,8 +102,9 @@ restricts you to having exactly one processor per replica. For more
 information, see the documentation for the <A HREF = "neb.html">neb</A> command.  In
 the current LAMMPS implementation of TAD, all the non-NEB TAD
 operations are performed on the first partition, while the other
-partitions remain idle. See <A HREF = "Section_howto.html#howto_5">this section</A>
+partitions remain idle. See <A HREF = "Section_howto.html#howto_5">Section_howto
-of the manual for further discussion of multi-replica simulations.
+5</A> of the manual for further discussion of
+multi-replica simulations.
 </P>
 <P>A TAD run has several stages, which are repeated each time an event is
 performed.  The logic for a TAD run is as follows:

doc/tad.txt

@@ -91,8 +91,9 @@ restricts you to having exactly one processor per replica. For more
 information, see the documentation for the "neb"_neb.html command.  In
 the current LAMMPS implementation of TAD, all the non-NEB TAD
 operations are performed on the first partition, while the other
-partitions remain idle. See "this section"_Section_howto.html#howto_5
+partitions remain idle. See "Section_howto
-of the manual for further discussion of multi-replica simulations.
+5"_Section_howto.html#howto_5 of the manual for further discussion of
+multi-replica simulations.
 
 
 A TAD run has several stages, which are repeated each time an event is

doc/temper.html

@@ -35,11 +35,11 @@ replicas (ensembles) of a system.  Two or more replicas must be used.
 </P>
 <P>Each replica runs on a partition of one or more processors.  Processor
 partitions are defined at run-time using the -partition command-line
-switch; see <A HREF = "Section_start.html#start_6">this section</A> of the manual.
+switch; see <A HREF = "Section_start.html#start_6">Section_start 6</A> of the
-Note that if you have MPI installed, you can run a multi-replica
+manual.  Note that if you have MPI installed, you can run a
-simulation with more replicas (partitions) than you have physical
+multi-replica simulation with more replicas (partitions) than you have
-processors, e.g you can run a 10-replica simulation on one or two
+physical processors, e.g you can run a 10-replica simulation on one or
-processors.  You will simply not get the performance speed-up you
+two processors.  You will simply not get the performance speed-up you
 would see with one or more physical processors per replica.  See <A HREF = "Section_howto.html#howto_5">this
 section</A> of the manual for further
 discussion.

doc/temper.txt

@@ -32,11 +32,11 @@ replicas (ensembles) of a system.  Two or more replicas must be used.
 
 Each replica runs on a partition of one or more processors.  Processor
 partitions are defined at run-time using the -partition command-line
-switch; see "this section"_Section_start.html#start_6 of the manual.
+switch; see "Section_start 6"_Section_start.html#start_6 of the
-Note that if you have MPI installed, you can run a multi-replica
+manual.  Note that if you have MPI installed, you can run a
-simulation with more replicas (partitions) than you have physical
+multi-replica simulation with more replicas (partitions) than you have
-processors, e.g you can run a 10-replica simulation on one or two
+physical processors, e.g you can run a 10-replica simulation on one or
-processors.  You will simply not get the performance speed-up you
+two processors.  You will simply not get the performance speed-up you
 would see with one or more physical processors per replica.  See "this
 section"_Section_howto.html#howto_5 of the manual for further
 discussion.