git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4107 f3b2605a-c512-4ea7-a41b-209d697bcdaa

2010-05-07 15:11:21 +00:00
parent 4930af351a
commit c5ea28b372
84 changed files with 208 additions and 198 deletions
--- a/doc/Manual.html
+++ b/doc/Manual.html
@ -33,7 +33,7 @@ National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
 under the terms of the GNU Public License (GPL).
 </P>
-<P>The primary developers of LAMMPS are <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul
+<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul
 Crozier, and Aidan Thompson who can be contacted at
 sjplimp,pscrozi,athomps at sandia.gov.  The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
 http://lammps.sandia.gov has more information about the code and its
@ -100,7 +100,7 @@ listed above.
 <BR>
  2.8 <A HREF = "Section_start.html#2_8">Running on GPUs</A> 
 <BR>
-  2.9 <A HREF = "2_9">Tips for users of previous versions</A> 
+  2.9 <A HREF = "Section_start.html#2_9">Tips for users of previous versions</A> 
 <BR></UL>
 <LI><A HREF = "Section_commands.html">Commands</A> 
@ -148,7 +148,7 @@ listed above.
 <BR>
  4.16 <A HREF = "Section_howto.html#4_16">Thermostatting, barostatting, and compute temperature</A> 
 <BR>
-  4.17 <A HREF = "4_17">Walls</A> 
+  4.17 <A HREF = "Section_howto.html#4_17">Walls</A> 
 <BR></UL>
 <LI><A HREF = "Section_example.html">Example problems</A> 
@ -247,6 +247,10 @@ listed above.
--- a/doc/Manual.txt
+++ b/doc/Manual.txt
@ -36,7 +36,7 @@ sjplimp,pscrozi,athomps at sandia.gov.  The "LAMMPS WWW Site"_lws at
 http://lammps.sandia.gov has more information about the code and its
 uses.
-:link(sjp,http://www.cs.sandia.gov/~sjplimp)
+:link(sjp,http://www.sandia.gov/~sjplimp)
 :line
@ -134,6 +134,7 @@ listed above.
 :link(2_6,Section_start.html#2_6)
 :link(2_7,Section_start.html#2_7)
 :link(2_8,Section_start.html#2_8)
 :link(2_9,Section_start.html#2_9)
 :link(3_1,Section_commands.html#3_1)
 :link(3_2,Section_commands.html#3_2)
@ -157,6 +158,7 @@ listed above.
 :link(4_14,Section_howto.html#4_14)
 :link(4_15,Section_howto.html#4_15)
 :link(4_16,Section_howto.html#4_16)
 :link(4_17,Section_howto.html#4_17)
 :link(9_1,Section_errors.html#9_1)
 :link(9_2,Section_errors.html#9_2)
--- a/doc/Section_howto.html
+++ b/doc/Section_howto.html
@ -639,12 +639,12 @@ files.  The second is the <A HREF = "Section_tools.html#arc">lmp2arc tool</A> wh
 converts LAMMPS dump files into Accelrys' Insight MD program files.
 The third is the <A HREF = "Section_tools.html#cfg">lmp2cfg tool</A> which converts
 LAMMPS dump files into CFG files which can be read into the
-<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer.
+<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualizer.
 </P>
 <P>A Python-based toolkit distributed by our group can read native LAMMPS
 dump files, including custom dump files with additional columns of
 user-specified atom information, and convert them to various formats
-or pipe them into visualization software directly.  See the <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py
+or pipe them into visualization software directly.  See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py
 WWW site</A> for details.  Specifically, Pizza.py can convert
 LAMMPS dump files into PDB, XYZ, <A HREF = "http://www.ensight.com">Ensight</A>, and VTK formats.
 Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
@ -861,7 +861,7 @@ that generate torque:
 <LI><A HREF = "pair_gran.html">pair_style gran/no_history</A>
 <LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A>
 <LI><A HREF = "pair_gayberne.html">pair_style gayberne</A>
-<LI><A HREF = "pair_resuared.html">pair_style resquared</A>
+<LI><A HREF = "pair_resquared.html">pair_style resquared</A>
 <LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> 
 </UL>
 <P>The <A HREF = "pair_gran.html">granular pair styles</A> are used with <A HREF = "atom_style.html">atom_style
@ -1254,7 +1254,7 @@ pressure</A> command calculates pressure.
 </UL>
 <P>All but the first 3 calculate velocity biases (i.e. advection
 velocities) that are removed when computing the thermal temperature.
-<A HREF = "fix_temp_sphere.html">Fix temp/sphere</A> and <A HREF = "fix_temp_asphere.html">fix
+<A HREF = "compute_temp_sphere.html">Compute temp/sphere</A> and <A HREF = "compute_temp_asphere.html">compute
 temp/asphere</A> compute kinetic energy for
 extended particles that includes rotational degrees of freedom.  They
 both allow, as an extra argument, which is another temperature compute
--- a/doc/Section_howto.txt
+++ b/doc/Section_howto.txt
@ -662,10 +662,10 @@ LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
 file format which can also be read by "VMD"_vmd for visualization.
 See the "dump"_dump.html command for more information on XTC files.
-:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
+:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
 :link(vmd,http://www.ks.uiuc.edu/Research/vmd)
 :link(ensight,http://www.ensight.com)
-:link(atomeye,http://164.107.79.177/Archive/Graphics/A)
+:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
 :line
@ -854,7 +854,7 @@ that generate torque:
 "pair_style gran/no_history"_pair_gran.html
 "pair_style dipole/cut"_pair_dipole.html
 "pair_style gayberne"_pair_gayberne.html
-"pair_style resquared"_pair_resuared.html
+"pair_style resquared"_pair_resquared.html
 "pair_style lubricate"_pair_lubricate.html :ul
 The "granular pair styles"_pair_gran.html are used with "atom_style
@ -1243,8 +1243,8 @@ pressure"_compute_pressure.html command calculates pressure.
 All but the first 3 calculate velocity biases (i.e. advection
 velocities) that are removed when computing the thermal temperature.
-"Fix temp/sphere"_fix_temp_sphere.html and "fix
+"Compute temp/sphere"_compute_temp_sphere.html and "compute
-temp/asphere"_fix_temp_asphere.html compute kinetic energy for
+temp/asphere"_compute_temp_asphere.html compute kinetic energy for
 extended particles that includes rotational degrees of freedom.  They
 both allow, as an extra argument, which is another temperature compute
 that subtracts a velocity bias.  This allows the translational
--- a/doc/Section_intro.html
+++ b/doc/Section_intro.html
@ -237,7 +237,7 @@ molecular dynamics options:
 <LI><A HREF = "temper.html">parallel tempering</A>
 <LI><A HREF = "prd.html">parallel replica dynamics</A>
 <LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
-<LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>
+<LI><A HREF = "pair_peri_pmb.html">Peridynamics mesoscale modeling</A>
 <LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics
 <LI><A HREF = "fix_ttm.html">two-temperature electron model</A> 
 </UL>
@ -485,7 +485,7 @@ add it to the Publications page of the <A HREF = "http://lammps.sandia.gov">LAMM
 for a picture or movie for the Pictures or Movies pages.
 </P>
 <P>The core group of LAMMPS developers is at Sandia National Labs.  They
-include <A HREF = "http://www.cs.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
+include <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
 be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
 </P>
 <P>Here are various folks who have made significant contributions to
--- a/doc/Section_intro.txt
+++ b/doc/Section_intro.txt
@ -233,7 +233,7 @@ coupled rigid body integration via the "POEMS"_fix_poems.html library
 "parallel tempering"_temper.html
 "parallel replica dynamics"_prd.html
 "Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
-"Peridynamics mesoscale modeling"_pair_peri.html
+"Peridynamics mesoscale modeling"_pair_peri_pmb.html
 "targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
 "two-temperature electron model"_fix_ttm.html :ul
@ -478,7 +478,7 @@ Here are various folks who have made significant contributions to
 features in LAMMPS.  The most recent contributions are at the top of
 the list.
-:link(sjp,http://www.cs.sandia.gov/~sjplimp)
+:link(sjp,http://www.sandia.gov/~sjplimp)
 pair yukawa/colloid : Randy Schunk (Sandia)
 fix wall/colloid : Jeremy Lechman (Sandia)
--- a/doc/Section_tools.html
+++ b/doc/Section_tools.html
@ -20,9 +20,9 @@ additional tools are provided with the LAMMPS distribution and are
 described in this section.
 </P>
 <P>Our group has also written and released a separate toolkit called
-<A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
+<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
 plotting, and visualization for LAMMPS simulations.  Pizza.py is
-written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">the
+written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the
 Pizza.py WWW site</A>.
 </P>
@ -172,7 +172,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
 </H4>
 <P>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
 files into a series of *.cfg files which can be read into the
-<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer.  See
+<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualizer.  See
 the README file for more information.
 </P>
 <P>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
@ -281,7 +281,7 @@ that perform common LAMMPS post-processing tasks, like
 <LI>sort the snapshots in a dump file by atom ID
 <LI>convert dump files into XYZ, CFG, or PDB format for viz by other packages 
 </UL>
-<P>These are simple scripts built on <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> modules.  See the
+<P>These are simple scripts built on <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> modules.  See the
 README for more info on Pizza.py and how to use these scripts.
 </P>
 <HR>
--- a/doc/Section_tools.txt
+++ b/doc/Section_tools.txt
@ -22,7 +22,7 @@ plotting, and visualization for LAMMPS simulations.  Pizza.py is
 written in "Python"_python and is available for download from "the
 Pizza.py WWW site"_pizza.
-:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
+:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
 :link(python,http://www.python.org)
 Note that many users write their own setup or analysis tools or use
@ -168,7 +168,7 @@ lmp2cfg tool :h4,link(cfg)
 The lmp2cfg sub-directory contains a tool for converting LAMMPS output
 files into a series of *.cfg files which can be read into the
-"AtomEye"_http://164.107.79.177/Archive/Graphics/A visualizer.  See
+"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualizer.  See
 the README file for more information.
 This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
--- a/doc/compute_displace_atom.html
+++ b/doc/compute_displace_atom.html
@ -40,7 +40,7 @@ command had been issued:
 </P>
 <PRE>fix compute-ID_store_coord group-ID store/coord 
 </PRE>
-<P>See the <A HREF = "fix_coord_original.html">fix store/coord</A> command for details.
+<P>See the <A HREF = "fix_store_coord.html">fix store/coord</A> command for details.
 Note that the ID of the new fix is the compute-ID + underscore +
 "store_coord", and the group for the new fix is the same as the
 compute group.
--- a/doc/compute_displace_atom.txt
+++ b/doc/compute_displace_atom.txt
@ -37,7 +37,7 @@ command had been issued:
 fix compute-ID_store_coord group-ID store/coord :pre
-See the "fix store/coord"_fix_coord_original.html command for details.
+See the "fix store/coord"_fix_store_coord.html command for details.
 Note that the ID of the new fix is the compute-ID + underscore +
 "store_coord", and the group for the new fix is the same as the
 compute group.
--- a/doc/compute_erotate_asphere.html
+++ b/doc/compute_erotate_asphere.html
@ -63,7 +63,7 @@ particles, but they can be aspherical or spherical.
 </P>
 <P><B>Related commands:</B> none
 </P>
-<P><A HREF = "compute_rotate_sphere.html">compute erotate/sphere</A>
+<P><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
 </P>
 <P><B>Default:</B> none
 </P>
--- a/doc/compute_erotate_asphere.txt
+++ b/doc/compute_erotate_asphere.txt
@ -60,6 +60,6 @@ particles, but they can be aspherical or spherical.
 [Related commands:] none
-"compute erotate/sphere"_compute_rotate_sphere.html
+"compute erotate/sphere"_compute_erotate_sphere.html
 [Default:] none
--- a/doc/compute_erotate_sphere.html
+++ b/doc/compute_erotate_sphere.html
@ -56,7 +56,7 @@ contribute to the rotational energy.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "compute_rotate_asphere.html">compute erotate/asphere</A>
+<P><A HREF = "compute_erotate_asphere.html">compute erotate/asphere</A>
 </P>
 <P><B>Default:</B> none
 </P>
--- a/doc/compute_erotate_sphere.txt
+++ b/doc/compute_erotate_sphere.txt
@ -53,6 +53,6 @@ contribute to the rotational energy.
 [Related commands:]
-"compute erotate/asphere"_compute_rotate_asphere.html
+"compute erotate/asphere"_compute_erotate_asphere.html
 [Default:] none
--- a/doc/compute_heat_flux.html
+++ b/doc/compute_heat_flux.html
@ -34,7 +34,7 @@ or to calculate a thermal conductivity using the Green-Kubo formalism.
 </P>
 <P>See the <A HREF = "fix_thermal_conductivity.html">fix thermal/conductivity</A>
 command for details on how to compute thermal conductivity in an
-alternate way, via the Muller-Plathe method.  See the <A HREF = "fix_heat">fix
+alternate way, via the Muller-Plathe method.  See the <A HREF = "fix_heat.html">fix
 heat</A> command for a way to control the heat added or
 subtracted to a group of atoms.
 </P>
--- a/doc/compute_heat_flux.txt
+++ b/doc/compute_heat_flux.txt
@ -32,7 +32,7 @@ or to calculate a thermal conductivity using the Green-Kubo formalism.
 See the "fix thermal/conductivity"_fix_thermal_conductivity.html
 command for details on how to compute thermal conductivity in an
 alternate way, via the Muller-Plathe method.  See the "fix
-heat"_fix_heat command for a way to control the heat added or
+heat"_fix_heat.html command for a way to control the heat added or
 subtracted to a group of atoms.
 The compute takes three arguments which are IDs of other
--- a/doc/compute_modify.html
+++ b/doc/compute_modify.html
@ -47,7 +47,7 @@ this option.  The default is 2 or 3 for <A HREF = "dimension.html">2d or 3d
 systems</A> which is a correction factor for an ensemble
 of velocities with zero total linear momentum.  You can use a negative
 number for the <I>extra</I> parameter if you need to add
-degrees-of-freedom.  See the <A HREF = "compute_temp_aspher.html">compute
+degrees-of-freedom.  See the <A HREF = "compute_temp_asphere.html">compute
 temp/asphere</A> command for an example.
 </P>
 <P>The <I>dynamic</I> keyword determines whether the number of atoms N in the
--- a/doc/compute_modify.txt
+++ b/doc/compute_modify.txt
@ -41,7 +41,7 @@ systems"_dimension.html which is a correction factor for an ensemble
 of velocities with zero total linear momentum.  You can use a negative
 number for the {extra} parameter if you need to add
 degrees-of-freedom.  See the "compute
-temp/asphere"_compute_temp_aspher.html command for an example.
+temp/asphere"_compute_temp_asphere.html command for an example.
 The {dynamic} keyword determines whether the number of atoms N in the
 compute group is re-computed each time a temperature is computed.
--- a/doc/compute_temp_com.html
+++ b/doc/compute_temp_com.html
@ -57,7 +57,7 @@ that performs thermostatting then this bias will be subtracted from
 each atom, thermostatting of the remaining thermal velocity will be
 performed, and the bias will be added back in.  Thermostatting fixes
 that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
-temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
 temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
 langevin</A>.
 </P>
--- a/doc/compute_temp_com.txt
+++ b/doc/compute_temp_com.txt
@ -55,7 +55,7 @@ each atom, thermostatting of the remaining thermal velocity will be
 performed, and the bias will be added back in.  Thermostatting fixes
 that work in this way include "fix nvt"_fix_nh.html, "fix
 temp/rescale"_fix_temp_rescale.html, "fix
-temp/berendsen"_fix_temp_berendsen, and "fix
+temp/berendsen"_fix_temp_berendsen.html, and "fix
 langevin"_fix_langevin.html.
 This compute subtracts out degrees-of-freedom due to fixes that
--- a/doc/compute_temp_deform.html
+++ b/doc/compute_temp_deform.html
@ -81,7 +81,7 @@ command that performs thermostatting then this bias will be subtracted
 from each atom, thermostatting of the remaining thermal velocity will
 be performed, and the bias will be added back in.  Thermostatting
 fixes that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
-temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
 temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
 langevin</A>.
 </P>
--- a/doc/compute_temp_deform.txt
+++ b/doc/compute_temp_deform.txt
@ -79,7 +79,7 @@ from each atom, thermostatting of the remaining thermal velocity will
 be performed, and the bias will be added back in.  Thermostatting
 fixes that work in this way include "fix nvt"_fix_nh.html, "fix
 temp/rescale"_fix_temp_rescale.html, "fix
-temp/berendsen"_fix_temp_berendsen, and "fix
+temp/berendsen"_fix_temp_berendsen.html, and "fix
 langevin"_fix_langevin.html.
 This compute subtracts out degrees-of-freedom due to fixes that
--- a/doc/compute_temp_partial.html
+++ b/doc/compute_temp_partial.html
@ -57,7 +57,7 @@ that performs thermostatting then this bias will be subtracted from
 each atom, thermostatting of the remaining thermal velocity will be
 performed, and the bias will be added back in.  Thermostatting fixes
 that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
-temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
 temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
 langevin</A>.
 </P>
--- a/doc/compute_temp_partial.txt
+++ b/doc/compute_temp_partial.txt
@ -55,7 +55,7 @@ each atom, thermostatting of the remaining thermal velocity will be
 performed, and the bias will be added back in.  Thermostatting fixes
 that work in this way include "fix nvt"_fix_nh.html, "fix
 temp/rescale"_fix_temp_rescale.html, "fix
-temp/berendsen"_fix_temp_berendsen, and "fix
+temp/berendsen"_fix_temp_berendsen.html, and "fix
 langevin"_fix_langevin.html.
 This compute subtracts out degrees-of-freedom due to fixes that
--- a/doc/compute_temp_profile.html
+++ b/doc/compute_temp_profile.html
@ -95,7 +95,7 @@ command that performs thermostatting then this bias will be subtracted
 from each atom, thermostatting of the remaining thermal velocity will
 be performed, and the bias will be added back in.  Thermostatting
 fixes that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
-temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
 temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
 langevin</A>.
 </P>
--- a/doc/compute_temp_profile.txt
+++ b/doc/compute_temp_profile.txt
@ -88,7 +88,7 @@ from each atom, thermostatting of the remaining thermal velocity will
 be performed, and the bias will be added back in.  Thermostatting
 fixes that work in this way include "fix nvt"_fix_nh.html, "fix
 temp/rescale"_fix_temp_rescale.html, "fix
-temp/berendsen"_fix_temp_berendsen, and "fix
+temp/berendsen"_fix_temp_berendsen.html, and "fix
 langevin"_fix_langevin.html.
 This compute subtracts out degrees-of-freedom due to fixes that
--- a/doc/compute_temp_ramp.html
+++ b/doc/compute_temp_ramp.html
@ -76,7 +76,7 @@ command that performs thermostatting then this bias will be subtracted
 from each atom, thermostatting of the remaining thermal velocity will
 be performed, and the bias will be added back in.  Thermostatting
 fixes that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
-temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
+temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
 temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
 langevin</A>.
 </P>
--- a/doc/compute_temp_ramp.txt
+++ b/doc/compute_temp_ramp.txt
@ -73,7 +73,7 @@ from each atom, thermostatting of the remaining thermal velocity will
 be performed, and the bias will be added back in.  Thermostatting
 fixes that work in this way include "fix nvt"_fix_nh.html, "fix
 temp/rescale"_fix_temp_rescale.html, "fix
-temp/berendsen"_fix_temp_berendsen, and "fix
+temp/berendsen"_fix_temp_berendsen.html, and "fix
 langevin"_fix_langevin.html.
 This compute subtracts out degrees-of-freedom due to fixes that
--- a/doc/compute_temp_region.html
+++ b/doc/compute_temp_region.html
@ -66,7 +66,7 @@ compute is used with a fix command that performs thermostatting then
 this bias will be subtracted from each atom, thermostatting of the
 remaining thermal velocity will be performed, and the bias will be
 added back in.  Thermostatting fixes that work in this way include
-<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
+<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
 temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
 langevin</A>.  This means any of the thermostatting
 fixes can operate on a geometric region of atoms, as defined by this
--- a/doc/compute_temp_region.txt
+++ b/doc/compute_temp_region.txt
@ -64,7 +64,7 @@ this bias will be subtracted from each atom, thermostatting of the
 remaining thermal velocity will be performed, and the bias will be
 added back in.  Thermostatting fixes that work in this way include
 "fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
-temp/berendsen"_fix_temp_berendsen, and "fix
+temp/berendsen"_fix_temp_berendsen.html, and "fix
 langevin"_fix_langevin.html.  This means any of the thermostatting
 fixes can operate on a geometric region of atoms, as defined by this
 compute.
--- a/doc/dump.html
+++ b/doc/dump.html
@ -123,7 +123,7 @@ individual values and the file itself.
 <P>The <I>atom</I>, <I>local</I>, and <I>custom</I> styles create files in a simple text
 format that is self-explanatory when viewing a dump file.  Many of the
 LAMMPS <A HREF = "Section_tools.html">post-processing tools</A>, including
-<A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>, work with
+<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>, work with
 this format.  
 </P>
 <P>For post-processing purposes the <I>atom</I> and <I>custom</I> text files are
--- a/doc/dump.txt
+++ b/doc/dump.txt
@ -113,7 +113,7 @@ individual values and the file itself.
 The {atom}, {local}, and {custom} styles create files in a simple text
 format that is self-explanatory when viewing a dump file.  Many of the
 LAMMPS "post-processing tools"_Section_tools.html, including
-"Pizza.py"_http://www.cs.sandia.gov/~sjplimp/pizza.html, work with
+"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with
 this format.  
 For post-processing purposes the {atom} and {custom} text files are
--- a/doc/fix_addforce.html
+++ b/doc/fix_addforce.html
@ -47,12 +47,12 @@ the group.  This command can be used to give an additional push to
 atoms in a simulation, such as for a simulation of Poiseuille flow in
 a channel.
 </P>
-<P>Any of the 3 quantities defining the force components can be
+<P>Any of the 3 quantities defining the force components can be specified
-specified as an equal-style or atom-style <A HREF = "variable">variable</A>, namely
+as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>,
-<I>fx</I>, <I>fy</I>, <I>fz</I>.  If the value is a variable, it should be specified
+<I>fy</I>, <I>fz</I>.  If the value is a variable, it should be specified as
-as v_ID, where ID is the variable ID.  In this case, the variable will
+v_ID, where ID is the variable ID.  In this case, the variable will be
-be evaluated each timestep, and its value used to determine the
+evaluated each timestep, and its value used to determine the force
-force component.
+component.
 </P>
 <P>Equal-style variables can specify formulas with various mathematical
 functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
--- a/doc/fix_addforce.txt
+++ b/doc/fix_addforce.txt
@ -37,12 +37,12 @@ the group.  This command can be used to give an additional push to
 atoms in a simulation, such as for a simulation of Poiseuille flow in
 a channel.
-Any of the 3 quantities defining the force components can be
+Any of the 3 quantities defining the force components can be specified
-specified as an equal-style or atom-style "variable"_variable, namely
+as an equal-style or atom-style "variable"_variable.html, namely {fx},
-{fx}, {fy}, {fz}.  If the value is a variable, it should be specified
+{fy}, {fz}.  If the value is a variable, it should be specified as
-as v_ID, where ID is the variable ID.  In this case, the variable will
+v_ID, where ID is the variable ID.  In this case, the variable will be
-be evaluated each timestep, and its value used to determine the
+evaluated each timestep, and its value used to determine the force
-force component.
+component.
 Equal-style variables can specify formulas with various mathematical
 functions, and include "thermo_style"_thermo_style.html command
--- a/doc/fix_atc.html
+++ b/doc/fix_atc.html
@ -205,7 +205,7 @@ conditions.
 </P>
 <UL><LI><A HREF = "USER/atc/man_hardy_fields.html">fix_modify AtC transfer fields</A>
 <LI><A HREF = "USER/atc/man_hardy_gradients.html">fix_modify AtC transfer gradients</A>
-<LI><A HREF = "USER/atc/man_hardy_rates.htm">fix_modify AtC transfer rates</A>
+<LI><A HREF = "USER/atc/man_hardy_rates.html">fix_modify AtC transfer rates</A>
 <LI><A HREF = "USER/atc/man_hardy_computes.html">fix_modify AtC transfer computes</A>
 <LI><A HREF = "USER/atc/man_hardy_set.html">fix_modify AtC set</A>
 <LI><A HREF = "USER/atc/man_hardy_on_the_fly.html">fix_modify AtC transfer on_the_fly</A>
@ -214,7 +214,7 @@ conditions.
 </UL>
 <P>miscellaneous fix_modify commands:
 </P>
-<UL><LI><A HREF = "USER/atc/man_atom_element_map.htm">fix_modify AtC transfer atom_element_map</A>
+<UL><LI><A HREF = "USER/atc/man_atom_element_map.html">fix_modify AtC transfer atom_element_map</A>
 <LI><A HREF = "USER/atc/man_neighbor_reset_frequency.html">fix_modify AtC transfer neighbor_reset_frequency</A> 
 </UL>
 <P><B>Default:</B> none
--- a/doc/fix_atc.txt
+++ b/doc/fix_atc.txt
@ -198,7 +198,7 @@ fix_modify commands for post-processing:
 "fix_modify AtC transfer fields"_USER/atc/man_hardy_fields.html
 "fix_modify AtC transfer gradients"_USER/atc/man_hardy_gradients.html
-"fix_modify AtC transfer rates"_USER/atc/man_hardy_rates.htm
+"fix_modify AtC transfer rates"_USER/atc/man_hardy_rates.html
 "fix_modify AtC transfer computes"_USER/atc/man_hardy_computes.html
 "fix_modify AtC set"_USER/atc/man_hardy_set.html
 "fix_modify AtC transfer on_the_fly"_USER/atc/man_hardy_on_the_fly.html
@ -207,7 +207,7 @@ fix_modify commands for post-processing:
 miscellaneous fix_modify commands:
-"fix_modify AtC transfer atom_element_map"_USER/atc/man_atom_element_map.htm
+"fix_modify AtC transfer atom_element_map"_USER/atc/man_atom_element_map.html
 "fix_modify AtC transfer neighbor_reset_frequency"_USER/atc/man_neighbor_reset_frequency.html :ul
 [Default:] none
--- a/doc/fix_aveforce.html
+++ b/doc/fix_aveforce.html
@ -56,9 +56,9 @@ same as specifying a 0.0 value, since that sets all forces to the same
 average value without adding in any additional force.
 </P>
 <P>Any of the 3 quantities defining the force components can be specified
-as an equal-style <A HREF = "variable">variable</A>, namely <I>fx</I>, <I>fy</I>, <I>fz</I>.  If
+as an equal-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>, <I>fy</I>, <I>fz</I>.
-the value is a variable, it should be specified as v_ID, where ID is
+If the value is a variable, it should be specified as v_ID, where ID
-the variable ID.  In this case, the variable will be evaluated each
+is the variable ID.  In this case, the variable will be evaluated each
 timestep, and its value used to determine the average force.
 </P>
 <P>Equal-style variables can specify formulas with various mathematical
--- a/doc/fix_aveforce.txt
+++ b/doc/fix_aveforce.txt
@ -46,9 +46,9 @@ same as specifying a 0.0 value, since that sets all forces to the same
 average value without adding in any additional force.
 Any of the 3 quantities defining the force components can be specified
-as an equal-style "variable"_variable, namely {fx}, {fy}, {fz}.  If
+as an equal-style "variable"_variable.html, namely {fx}, {fy}, {fz}.
-the value is a variable, it should be specified as v_ID, where ID is
+If the value is a variable, it should be specified as v_ID, where ID
-the variable ID.  In this case, the variable will be evaluated each
+is the variable ID.  In this case, the variable will be evaluated each
 timestep, and its value used to determine the average force.
 Equal-style variables can specify formulas with various mathematical
--- a/doc/fix_deform.html
+++ b/doc/fix_deform.html
@ -419,7 +419,7 @@ not remapped even if <I>remap</I> is set to <I>v</I>, since <A HREF = "fix_nvt_s
 nvt/sllod</A> does not currently do anything special
 for rigid particles.  If you wish to perform a NEMD simulation of
 rigid particles, you can either thermostat them independently or
-include a background fluid and thermostat the fluid via <A HREF = "fix_nvt_sllod">fix
+include a background fluid and thermostat the fluid via <A HREF = "fix_nvt_sllod.html">fix
 nvt/sllod</A>.
 </P>
 <P>The <I>units</I> keyword determines the meaning of the distance units used
--- a/doc/fix_deform.txt
+++ b/doc/fix_deform.txt
@ -410,7 +410,7 @@ nvt/sllod"_fix_nvt_sllod.html does not currently do anything special
 for rigid particles.  If you wish to perform a NEMD simulation of
 rigid particles, you can either thermostat them independently or
 include a background fluid and thermostat the fluid via "fix
-nvt/sllod"_fix_nvt_sllod.
+nvt/sllod"_fix_nvt_sllod.html.
 The {units} keyword determines the meaning of the distance units used
 to define various arguments.  A {box} value selects standard distance
--- a/doc/fix_heat.html
+++ b/doc/fix_heat.html
@ -67,8 +67,8 @@ or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A> in that energy is
 added/subtracted continually.  Thus if there isn't another mechanism
 in place to counterbalance this effect, the entire system will heat or
 cool continuously.  You can use multiple heat fixes so that the net
-energy change is 0.0 or use <A HREF = "fix_viscous">fix viscous</A> to drain energy
+energy change is 0.0 or use <A HREF = "fix_viscous.html">fix viscous</A> to drain
-from the system.
+energy from the system.
 </P>
 <P>This fix does not change the coordinates of its atoms; it only scales
 their velocities.  Thus you must still use an integration fix
--- a/doc/fix_heat.txt
+++ b/doc/fix_heat.txt
@ -57,8 +57,8 @@ or "fix temp/rescale"_fix_temp_rescale.html in that energy is
 added/subtracted continually.  Thus if there isn't another mechanism
 in place to counterbalance this effect, the entire system will heat or
 cool continuously.  You can use multiple heat fixes so that the net
-energy change is 0.0 or use "fix viscous"_fix_viscous to drain energy
+energy change is 0.0 or use "fix viscous"_fix_viscous.html to drain
-from the system.
+energy from the system.
 This fix does not change the coordinates of its atoms; it only scales
 their velocities.  Thus you must still use an integration fix
--- a/doc/fix_indent.html
+++ b/doc/fix_indent.html
@ -98,8 +98,8 @@ the plane's current position will feel no force.  Vice versa if <I>side</I>
 is specified as <I>hi</I>.
 </P>
 <P>Any of the 4 quantities defining a spherical indenter's geometry can
-be specified as an equal-style <A HREF = "variable">variable</A>, namely <I>x</I>, <I>y</I>,
+be specified as an equal-style <A HREF = "variable.html">variable</A>, namely <I>x</I>,
-<I>z</I>, or <I>R</I>.  Similarly, for a cylindrical indenter, any of <I>c1</I>,
+<I>y</I>, <I>z</I>, or <I>R</I>.  Similarly, for a cylindrical indenter, any of <I>c1</I>,
 <I>c2</I>, or <I>R</I>, can be a variable.  For a planar indenter, <I>pos</I> can be
 a variable.  If the value is a variable, it should be specified as
 v_ID, where ID is the variable ID.  In this case, the variable will be
--- a/doc/fix_indent.txt
+++ b/doc/fix_indent.txt
@ -89,8 +89,8 @@ the plane's current position will feel no force.  Vice versa if {side}
 is specified as {hi}.
 Any of the 4 quantities defining a spherical indenter's geometry can
-be specified as an equal-style "variable"_variable, namely {x}, {y},
+be specified as an equal-style "variable"_variable.html, namely {x},
-{z}, or {R}.  Similarly, for a cylindrical indenter, any of {c1},
+{y}, {z}, or {R}.  Similarly, for a cylindrical indenter, any of {c1},
 {c2}, or {R}, can be a variable.  For a planar indenter, {pos} can be
 a variable.  If the value is a variable, it should be specified as
 v_ID, where ID is the variable ID.  In this case, the variable will be
--- a/doc/fix_nh.html
+++ b/doc/fix_nh.html
@ -51,7 +51,7 @@ keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or
 <PRE>fix 1 all nvt temp 300.0 300.0 100.0
 fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
 fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0
-fix 2 ice nph temp 273.15 273.15 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 
+fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 
 </PRE>
 <P><B>Description:</B>
 </P>
--- a/doc/fix_nh.txt
+++ b/doc/fix_nh.txt
@ -43,7 +43,7 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {y
 fix 1 all nvt temp 300.0 300.0 100.0
 fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
 fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0
-fix 2 ice nph temp 273.15 273.15 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre
+fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre
 [Description:]
--- a/doc/fix_press_berendsen.html
+++ b/doc/fix_press_berendsen.html
@ -75,10 +75,10 @@ thermostatting and barostatting.
 ability to specify the 3 diagonal components of an external stress
 tensor, and to couple various of these components together so that the
 dimensions they represent are varied together during a
-constant-pressure simulation.  Unlike the <A HREF = "fix_npt.html">fix npt</A> and
+constant-pressure simulation.  Unlike the <A HREF = "fix_nh.html">fix npt</A> and
-<A HREF = "fix_nph.html">fix nph</A> commands, this fix cannot be used with
+<A HREF = "fix_nh.html">fix nph</A> commands, this fix cannot be used with triclinic
-triclinic (non-orthogonal) simulation boxes to control all 6
+(non-orthogonal) simulation boxes to control all 6 components of the
-components of the general pressure tensor.
+general pressure tensor.
 </P>
 <P>The target pressures for each of the 3 diagonal components of the
 stress tensor can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I>,
--- a/doc/fix_press_berendsen.txt
+++ b/doc/fix_press_berendsen.txt
@ -69,10 +69,10 @@ The barostat is specified using one or more of the {iso}, {aniso},
 ability to specify the 3 diagonal components of an external stress
 tensor, and to couple various of these components together so that the
 dimensions they represent are varied together during a
-constant-pressure simulation.  Unlike the "fix npt"_fix_npt.html and
+constant-pressure simulation.  Unlike the "fix npt"_fix_nh.html and
-"fix nph"_fix_nph.html commands, this fix cannot be used with
+"fix nph"_fix_nh.html commands, this fix cannot be used with triclinic
-triclinic (non-orthogonal) simulation boxes to control all 6
+(non-orthogonal) simulation boxes to control all 6 components of the
-components of the general pressure tensor.
+general pressure tensor.
 The target pressures for each of the 3 diagonal components of the
 stress tensor can be specified independently via the {x}, {y}, {z},
--- a/doc/fix_rigid.html
+++ b/doc/fix_rigid.html
@ -251,14 +251,14 @@ modified when the center-of-mass of the rigid body moves across a
 periodic boundary.  They are not incremented/decremented as they would
 be for non-rigid atoms.  This change does not affect dynamics, but
 means that any diagnostic computation based on the atomic image flag
-values must be adjusted accordingly.  For example, the <A HREF = "fix_msd.html">fix
+values must be adjusted accordingly.  For example, the <A HREF = "compute_msd.html">compute
 msd</A> will not compute the expected mean-squared
 displacement for such atoms, and the image flag values written to a
 <A HREF = "dump.html">dump file</A> will be different than they would be if the
 atoms were not in a rigid body.  It also means that if you have bonds
 between a pair of rigid bodies and the bond straddles a periodic
-boundary, you cannot use the <A HREF = "replicate">replicate</A> command to increase
+boundary, you cannot use the <A HREF = "replicate.html">replicate</A> command to
-the system size.
+increase the system size.
 </P>
 <HR>
--- a/doc/fix_rigid.txt
+++ b/doc/fix_rigid.txt
@ -240,14 +240,14 @@ modified when the center-of-mass of the rigid body moves across a
 periodic boundary.  They are not incremented/decremented as they would
 be for non-rigid atoms.  This change does not affect dynamics, but
 means that any diagnostic computation based on the atomic image flag
-values must be adjusted accordingly.  For example, the "fix
+values must be adjusted accordingly.  For example, the "compute
-msd"_fix_msd.html will not compute the expected mean-squared
+msd"_compute_msd.html will not compute the expected mean-squared
 displacement for such atoms, and the image flag values written to a
 "dump file"_dump.html will be different than they would be if the
 atoms were not in a rigid body.  It also means that if you have bonds
 between a pair of rigid bodies and the bond straddles a periodic
-boundary, you cannot use the "replicate"_replicate command to increase
+boundary, you cannot use the "replicate"_replicate.html command to
-the system size.
+increase the system size.
 :line
--- a/doc/fix_setforce.html
+++ b/doc/fix_setforce.html
@ -49,12 +49,12 @@ force, assuming their initial velocity zero.
 <P>Any of the fx,fy,fz values can be specified as NULL which means do not
 alter the force component in that dimension.
 </P>
-<P>Any of the 3 quantities defining the force components can be
+<P>Any of the 3 quantities defining the force components can be specified
-specified as an equal-style or atom-style <A HREF = "variable">variable</A>, namely
+as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>,
-<I>fx</I>, <I>fy</I>, <I>fz</I>.  If the value is a variable, it should be specified
+<I>fy</I>, <I>fz</I>.  If the value is a variable, it should be specified as
-as v_ID, where ID is the variable ID.  In this case, the variable will
+v_ID, where ID is the variable ID.  In this case, the variable will be
-be evaluated each timestep, and its value used to determine the
+evaluated each timestep, and its value used to determine the force
-force component.
+component.
 </P>
 <P>Equal-style variables can specify formulas with various mathematical
 functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
--- a/doc/fix_setforce.txt
+++ b/doc/fix_setforce.txt
@ -39,12 +39,12 @@ force, assuming their initial velocity zero.
 Any of the fx,fy,fz values can be specified as NULL which means do not
 alter the force component in that dimension.
-Any of the 3 quantities defining the force components can be
+Any of the 3 quantities defining the force components can be specified
-specified as an equal-style or atom-style "variable"_variable, namely
+as an equal-style or atom-style "variable"_variable.html, namely {fx},
-{fx}, {fy}, {fz}.  If the value is a variable, it should be specified
+{fy}, {fz}.  If the value is a variable, it should be specified as
-as v_ID, where ID is the variable ID.  In this case, the variable will
+v_ID, where ID is the variable ID.  In this case, the variable will be
-be evaluated each timestep, and its value used to determine the
+evaluated each timestep, and its value used to determine the force
-force component.
+component.
 Equal-style variables can specify formulas with various mathematical
 functions, and include "thermo_style"_thermo_style.html command
--- a/doc/fix_store_coord.html
+++ b/doc/fix_store_coord.html
@ -87,7 +87,7 @@ minimization</A>.
 <P><B>Related commands:</B>
 </P>
 <P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "compute_displace_atom.html">compute
-displace/atom</A>, <A HREF = "compute_store_force.html">compute
+displace/atom</A>, <A HREF = "fix_store_force.html">fix
 store/force</A>
 </P>
 <P><B>Default:</B>
--- a/doc/fix_store_coord.txt
+++ b/doc/fix_store_coord.txt
@ -79,8 +79,8 @@ minimization"_minimize.html.
 [Related commands:]
 "compute msd"_compute_msd.html, "compute
-displace/atom"_compute_displace_atom.html, "compute
+displace/atom"_compute_displace_atom.html, "fix
-store/force"_compute_store_force.html
+store/force"_fix_store_force.html
 [Default:]
--- a/doc/fix_store_force.html
+++ b/doc/fix_store_force.html
@ -70,7 +70,7 @@ minimization</A>.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "compute_store_coord.html">compute store/coord</A>
+<P><A HREF = "fix_store_coord.html">fix store/coord</A>
 </P>
 <P><B>Default:</B> none
 </P>
--- a/doc/fix_store_force.txt
+++ b/doc/fix_store_force.txt
@ -67,6 +67,6 @@ minimization"_minimize.html.
 [Related commands:]
-"compute store/coord"_compute_store_coord.html
+"fix store/coord"_fix_store_coord.html
 [Default:] none
--- a/doc/fix_ttm.html
+++ b/doc/fix_ttm.html
@ -192,7 +192,7 @@ minimization</A>.
 <P><B>Restrictions:</B>
 </P>
 <P>This fix can only be used for 3d simulations and orthogonal
-simlulation boxes.  You must use periodic <A HREF = "doc/boundary.html">boundary</A>
+simlulation boxes.  You must use periodic <A HREF = "boundary.html">boundary</A>
 conditions with this fix.
 </P>
 <P><B>Related commands:</B>
--- a/doc/fix_ttm.txt
+++ b/doc/fix_ttm.txt
@ -189,7 +189,7 @@ minimization"_minimize.html.
 [Restrictions:]
 This fix can only be used for 3d simulations and orthogonal
-simlulation boxes.  You must use periodic "boundary"_doc/boundary.html
+simlulation boxes.  You must use periodic "boundary"_boundary.html
 conditions with this fix.
 [Related commands:]
--- a/doc/fix_wall_reflect.html
+++ b/doc/fix_wall_reflect.html
@ -60,14 +60,14 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
 <P>A reflecting wall should not be used with rigid bodies such as those
 defined by a "fix rigid" command.  This is because the wall/reflect
 displaces atoms directly rather than exerts a force on them.  For
-rigid bodies, use a soft wall instead, such as <A HREF = "fix_wall_lj93.html">fix
+rigid bodies, use a soft wall instead, such as <A HREF = "fix_wall.html">fix
 wall/lj93</A>.  LAMMPS will flag the use of a rigid
 fix with fix wall/reflect with a warning, but will not generate an
 error.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "fix_wall_lj93.html">fix wall/lj93</A> command
+<P><A HREF = "fix_wall.html">fix wall/lj93</A> command
 </P>
 <P><B>Default:</B> none
 </P>
--- a/doc/fix_wall_reflect.txt
+++ b/doc/fix_wall_reflect.txt
@ -58,13 +58,13 @@ A reflecting wall should not be used with rigid bodies such as those
 defined by a "fix rigid" command.  This is because the wall/reflect
 displaces atoms directly rather than exerts a force on them.  For
 rigid bodies, use a soft wall instead, such as "fix
-wall/lj93"_fix_wall_lj93.html.  LAMMPS will flag the use of a rigid
+wall/lj93"_fix_wall.html.  LAMMPS will flag the use of a rigid
 fix with fix wall/reflect with a warning, but will not generate an
 error.
 [Related commands:]
-"fix wall/lj93"_fix_wall_lj93.html command
+"fix wall/lj93"_fix_wall.html command
 [Default:] none
--- a/doc/group.html
+++ b/doc/group.html
@ -106,7 +106,7 @@ group.  This group cannot be deleted.
 <P><B>Related commands:</B>
 </P>
 <P><A HREF = "dump.html">dump</A>, <A HREF = "fix.html">fix</A>, <A HREF = "region.html">region</A>,
-<A HREF = "temperature.html">temperature</A>, <A HREF = "velocity.html">velocity</A>
+<A HREF = "velocity.html">velocity</A>
 </P>
 <P><B>Default:</B>
 </P>
--- a/doc/group.txt
+++ b/doc/group.txt
@ -101,7 +101,7 @@ There can be no more than 32 groups defined at one time, including
 [Related commands:]
 "dump"_dump.html, "fix"_fix.html, "region"_region.html,
-"temperature"_temperature.html, "velocity"_velocity.html
+"velocity"_velocity.html
 [Default:]
--- a/doc/kspace_style.html
+++ b/doc/kspace_style.html
@ -108,9 +108,10 @@ style <I>pppm/tip4p</I> and vice versa.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "pair_style.html">pair_style</A>
+<P><A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "pair_lj.html">pair_style
-lj/cut/coul/long, <A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/long,
+lj/cut/coul/long</A>, <A HREF = "pair_charmm.html">pair_style
-<A HREF = "pair_style">pair_style</A> lj/coul, <A HREF = "pair_style">pair_style</A> buck/coul
+lj/charmm/coul/long</A>, <A HREF = "pair_lj_coul.html">pair_style
 lj/coul</A>, <A HREF = "pair_buck.html">pair_style buck/coul/long</A>
 </P>
 <P><B>Default:</B>
 </P>
--- a/doc/kspace_style.txt
+++ b/doc/kspace_style.txt
@ -103,9 +103,10 @@ style {pppm/tip4p} and vice versa.
 [Related commands:]
-"kspace_modify"_kspace_modify.html, "pair_style"_pair_style.html
+"kspace_modify"_kspace_modify.html, "pair_style
-lj/cut/coul/long, "pair_style"_pair_style.html lj/charmm/coul/long,
+lj/cut/coul/long"_pair_lj.html, "pair_style
-"pair_style"_pair_style lj/coul, "pair_style"_pair_style buck/coul
+lj/charmm/coul/long"_pair_charmm.html, "pair_style
 lj/coul"_pair_lj_coul.html, "pair_style buck/coul/long"_pair_buck.html
 [Default:]
--- a/doc/lattice.html
+++ b/doc/lattice.html
@ -127,7 +127,7 @@ simulation box.
 scaled when mapping it into the simulation box.  I.e. it determines a
 multiplicative factor to apply to the unit cell, to convert it to a
 lattice of the desired size and distance units in the simulation box.
-The meaning of the <I>scale</I> argument depends on the <A HREF = "unit.html">units</A>
+The meaning of the <I>scale</I> argument depends on the <A HREF = "units.html">units</A>
 being used in your simulation.
 </P>
 <P>For all unit styles except <I>lj</I>, the scale argument is specified in
--- a/doc/lattice.txt
+++ b/doc/lattice.txt
@ -119,7 +119,7 @@ The {scale} argument determines how the size of the unit cell will be
 scaled when mapping it into the simulation box.  I.e. it determines a
 multiplicative factor to apply to the unit cell, to convert it to a
 lattice of the desired size and distance units in the simulation box.
-The meaning of the {scale} argument depends on the "units"_unit.html
+The meaning of the {scale} argument depends on the "units"_units.html
 being used in your simulation.
 For all unit styles except {lj}, the scale argument is specified in
--- a/doc/min_style.html
+++ b/doc/min_style.html
@ -1,5 +1,5 @@
 <HTML>
-<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Page</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Chapter_commands.html#comm">LAMMPS Commands</A> 
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Page</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> 
 </CENTER>
--- a/doc/min_style.txt
+++ b/doc/min_style.txt
@ -2,7 +2,7 @@
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Chapter_commands.html#comm)
+:link(lc,Section_commands.html#comm)
 :line
 min_style command :h3
--- a/doc/minimize.html
+++ b/doc/minimize.html
@ -170,13 +170,14 @@ minimum to the specified energy or force tolerance.
 </P>
 <P>Note that a cutoff Lennard-Jones potential (and others) can be shifted
 so that its energy is 0.0 at the cutoff via the
-<A HREF = "pair_modify">pair_modify</A> command.  See the doc pages for inidividual
+<A HREF = "pair_modify.html">pair_modify</A> command.  See the doc pages for
-<A HREF = "pair_style.html">pair styles</A> for details.  Note that Coulombic
+inidividual <A HREF = "pair_style.html">pair styles</A> for details.  Note that
-potentials always have a cutoff, unless versions with a long-range
+Coulombic potentials always have a cutoff, unless versions with a
-component are used (e.g. <A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A>).
+long-range component are used (e.g. <A HREF = "pair_lj.html">pair_style
-The CHARMM potentials go to 0.0 at the cutoff (e.g. <A HREF = "pair_charmm.html</I>">pair_style
+lj/cut/coul/long</A>).  The CHARMM potentials go to 0.0 at
-lj/charmm/coul/charmm</A>, as do the GROMACS potentials
+the cutoff (e.g. <A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A>),
-(e.g. <A HREF = "pair_gromacs.html</I>">pair_style lj/gromacs</A>.
+as do the GROMACS potentials (e.g. <A HREF = "pair_gromacs.html">pair_style
 lj/gromacs</A>).
 </P>
 <P>If a soft potential (<A HREF = "pair_soft.html">pair_style soft</A>) is used the
 Astop value is used for the prefactor (no time dependence).
--- a/doc/minimize.txt
+++ b/doc/minimize.txt
@ -167,13 +167,14 @@ minimum to the specified energy or force tolerance.
 Note that a cutoff Lennard-Jones potential (and others) can be shifted
 so that its energy is 0.0 at the cutoff via the
-"pair_modify"_pair_modify command.  See the doc pages for inidividual
+"pair_modify"_pair_modify.html command.  See the doc pages for
-"pair styles"_pair_style.html for details.  Note that Coulombic
+inidividual "pair styles"_pair_style.html for details.  Note that
-potentials always have a cutoff, unless versions with a long-range
+Coulombic potentials always have a cutoff, unless versions with a
-component are used (e.g. "pair_style lj/cut/coul/long"_pair_lj.html).
+long-range component are used (e.g. "pair_style
-The CHARMM potentials go to 0.0 at the cutoff (e.g. "pair_style
+lj/cut/coul/long"_pair_lj.html).  The CHARMM potentials go to 0.0 at
-lj/charmm/coul/charmm"_pair_charmm.html}, as do the GROMACS potentials
+the cutoff (e.g. "pair_style lj/charmm/coul/charmm"_pair_charmm.html),
-(e.g. "pair_style lj/gromacs"_pair_gromacs.html}.
+as do the GROMACS potentials (e.g. "pair_style
 lj/gromacs"_pair_gromacs.html).
 If a soft potential ("pair_style soft"_pair_soft.html) is used the
 Astop value is used for the prefactor (no time dependence).
--- a/doc/pair_dipole.html
+++ b/doc/pair_dipole.html
@ -120,8 +120,7 @@ LAMMPS</A> section for more info.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_dipole.html">fix nve/dipole</A>,
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
 <A HREF = "compute_temp_dipole.html">compute temp/dipole</A>
 </P>
 <P><B>Default:</B> none
 </P>
--- a/doc/pair_dipole.txt
+++ b/doc/pair_dipole.txt
@ -117,8 +117,7 @@ LAMMPS"_Section_start.html#2_3 section for more info.
 [Related commands:]
-"pair_coeff"_pair_coeff.html, "fix nve/dipole"_fix_nve_dipole.html,
+"pair_coeff"_pair_coeff.html
 "compute temp/dipole"_compute_temp_dipole.html
 [Default:] none
--- a/doc/pair_hybrid.html
+++ b/doc/pair_hybrid.html
@ -105,7 +105,7 @@ as described below.
 </P>
 <P>If you want there to be no interactions between a particular pair of
 atom types, you have 3 choices.  You can assign the type pair to some
-sub-style and use the <A HREF = "neigh_modify">neigh_modify exclude type</A>
+sub-style and use the <A HREF = "neigh_modify.html">neigh_modify exclude type</A>
 command.  You can assign it to some sub-style and set the coefficients
 so that there is effectively no interaction (e.g. epsilon = 0.0 in a
 LJ potential).  Or, for <I>hybrid</I> and <I>hybrid/overlay</I> simulations, you
@ -147,11 +147,11 @@ associated sub-style supports it.
 </P>
 <P>For the hybrid pair styles, the list of sub-styles and their
 respective settings are written to <A HREF = "restart.html">binary restart
-files</A>, so a pair_style command does not need to
+files</A>, so a <A HREF = "pair_style.html">pair_style</A> command does
-specified in an input script that reads a restart file.  However, the
+not need to specified in an input script that reads a restart file.
-coefficient information is not stored in the restart file.  Thus,
+However, the coefficient information is not stored in the restart
-pair_coeff commands need to be re-specified in the restart input
+file.  Thus, pair_coeff commands need to be re-specified in the
-script.
+restart input script.
 </P>
 <P>These pair styles support the use of the <I>inner</I>, <I>middle</I>, and
 <I>outer</I> keywords of the <A HREF = "run_style.html">run_style respa</A> command, if
@ -160,11 +160,11 @@ their sub-styles do.
 <P><B>Restrictions:</B>
 </P>
 <P>When using a long-range Coulombic solver (via the
-<A HREF = "kspace_style">kspace_style</A> command) with a hybrid pair_style, one or
+<A HREF = "kspace_style.html">kspace_style</A> command) with a hybrid pair_style,
-more sub-styles will be of the "long" variety, e.g. <I>lj/cut/coul/long</I>
+one or more sub-styles will be of the "long" variety,
-or <I>buck/coul/long</I>.  You must insure that the short-range Coulombic
+e.g. <I>lj/cut/coul/long</I> or <I>buck/coul/long</I>.  You must insure that the
-cutoff used by each of these long pair styles is the same or else
+short-range Coulombic cutoff used by each of these long pair styles is
-LAMMPS will generate an error.
+the same or else LAMMPS will generate an error.
 </P>
 <P><B>Related commands:</B>
 </P>
--- a/doc/pair_hybrid.txt
+++ b/doc/pair_hybrid.txt
@ -101,7 +101,7 @@ as described below.
 If you want there to be no interactions between a particular pair of
 atom types, you have 3 choices.  You can assign the type pair to some
-sub-style and use the "neigh_modify exclude type"_neigh_modify
+sub-style and use the "neigh_modify exclude type"_neigh_modify.html
 command.  You can assign it to some sub-style and set the coefficients
 so that there is effectively no interaction (e.g. epsilon = 0.0 in a
 LJ potential).  Or, for {hybrid} and {hybrid/overlay} simulations, you
@ -143,11 +143,11 @@ associated sub-style supports it.
 For the hybrid pair styles, the list of sub-styles and their
 respective settings are written to "binary restart
-files"_restart.html, so a pair_style command does not need to
+files"_restart.html, so a "pair_style"_pair_style.html command does
-specified in an input script that reads a restart file.  However, the
+not need to specified in an input script that reads a restart file.
-coefficient information is not stored in the restart file.  Thus,
+However, the coefficient information is not stored in the restart
-pair_coeff commands need to be re-specified in the restart input
+file.  Thus, pair_coeff commands need to be re-specified in the
-script.
+restart input script.
 These pair styles support the use of the {inner}, {middle}, and
 {outer} keywords of the "run_style respa"_run_style.html command, if
@ -156,11 +156,11 @@ their sub-styles do.
 [Restrictions:]
 When using a long-range Coulombic solver (via the
-"kspace_style"_kspace_style command) with a hybrid pair_style, one or
+"kspace_style"_kspace_style.html command) with a hybrid pair_style,
-more sub-styles will be of the "long" variety, e.g. {lj/cut/coul/long}
+one or more sub-styles will be of the "long" variety,
-or {buck/coul/long}.  You must insure that the short-range Coulombic
+e.g. {lj/cut/coul/long} or {buck/coul/long}.  You must insure that the
-cutoff used by each of these long pair styles is the same or else
+short-range Coulombic cutoff used by each of these long pair styles is
-LAMMPS will generate an error.
+the same or else LAMMPS will generate an error.
 [Related commands:]
--- a/doc/prd.html
+++ b/doc/prd.html
@ -280,7 +280,7 @@ for dephasing.
 of elapsed time to perform time-dependent operations.  Examples
 include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
 ave/spatial</A>.  Also <A HREF = "fix_dt_reset.html">fix
-dt/reset</A> and <A HREF = "fix_deposity.html">fix deposit</A>.
+dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
 </P>
 <P><B>Related commands:</B>
 </P>
--- a/doc/prd.txt
+++ b/doc/prd.txt
@ -267,7 +267,7 @@ This command cannot be used when any fixes are defined that keep track
 of elapsed time to perform time-dependent operations.  Examples
 include the "ave" fixes such as "fix
 ave/spatial"_fix_ave_spatial.html.  Also "fix
-dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposity.html.
+dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
 [Related commands:]
--- a/doc/reset_timestep.html
+++ b/doc/reset_timestep.html
@ -49,7 +49,7 @@ given after the reset_timestep command is used.
 of elapsed time to perform time-dependent operations.  Examples
 include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
 ave/spatial</A>.  Also <A HREF = "fix_dt_reset.html">fix
-dt/reset</A> and <A HREF = "fix_deposity.html">fix deposit</A>.
+dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
 </P>
 <P>This command cannot be used when any dynamic regions are defined via
 the <A HREF = "region.html">region</A> command, which have time-dependent position
--- a/doc/reset_timestep.txt
+++ b/doc/reset_timestep.txt
@ -46,7 +46,7 @@ This command cannot be used when any fixes are defined that keep track
 of elapsed time to perform time-dependent operations.  Examples
 include the "ave" fixes such as "fix
 ave/spatial"_fix_ave_spatial.html.  Also "fix
-dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposity.html.
+dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
 This command cannot be used when any dynamic regions are defined via
 the "region"_region.html command, which have time-dependent position
--- a/doc/set.html
+++ b/doc/set.html
@ -171,13 +171,14 @@ value for that dimension is unchanged.
 atoms have diffused one or more box lengths in various directions.
 This command can then reset the image values for atoms so that they
 are effectively inside the simulation box, e.g if a diffusion
-coefficient is about to be measured via the <A HREF = "fix_msd.html">fix msd</A>
+coefficient is about to be measured via the <A HREF = "compute_msd.html">compute
-command.  Care should be taken not to reset the image flags of two
+msd</A> command.  Care should be taken not to reset the
-atoms in a bond to the same value if the bond straddles a periodic
+image flags of two atoms in a bond to the same value if the bond
-boundary (rather they should be different by +/- 1).  This will not
+straddles a periodic boundary (rather they should be different by +/-
-affect the dynamics of a simulation, but may mess up analysis of the
+1).  This will not affect the dynamics of a simulation, but may mess
-trajectories if a LAMMPS diagnostic or your own analysis relies on the
+up analysis of the trajectories if a LAMMPS diagnostic or your own
-image flags to unwrap a molecule which straddles the periodic box.
+analysis relies on the image flags to unwrap a molecule which
 straddles the periodic box.
 </P>
 <P>For the <I>diameter</I> and <I>density</I> and <I>volume</I> keywords, the <A HREF = "atom_style.html">atom
 style</A> being used must support the use of those
--- a/doc/set.txt
+++ b/doc/set.txt
@ -166,13 +166,14 @@ This command can be useful after a system has been equilibrated and
 atoms have diffused one or more box lengths in various directions.
 This command can then reset the image values for atoms so that they
 are effectively inside the simulation box, e.g if a diffusion
-coefficient is about to be measured via the "fix msd"_fix_msd.html
+coefficient is about to be measured via the "compute
-command.  Care should be taken not to reset the image flags of two
+msd"_compute_msd.html command.  Care should be taken not to reset the
-atoms in a bond to the same value if the bond straddles a periodic
+image flags of two atoms in a bond to the same value if the bond
-boundary (rather they should be different by +/- 1).  This will not
+straddles a periodic boundary (rather they should be different by +/-
-affect the dynamics of a simulation, but may mess up analysis of the
+1).  This will not affect the dynamics of a simulation, but may mess
-trajectories if a LAMMPS diagnostic or your own analysis relies on the
+up analysis of the trajectories if a LAMMPS diagnostic or your own
-image flags to unwrap a molecule which straddles the periodic box.
+analysis relies on the image flags to unwrap a molecule which
 straddles the periodic box.
 For the {diameter} and {density} and {volume} keywords, the "atom
 style"_atom_style.html being used must support the use of those
--- a/doc/thermo_style.html
+++ b/doc/thermo_style.html
@ -181,7 +181,7 @@ components of velocity and/or include different degrees of freedom
 </P>
 <P>The potential energy of the system <I>pe</I> will include contributions
 from fixes if the <A HREF = "fix_modify.html">fix_modify thermo</A> option is set
-for a fix that calculates such a contribution.  For example, the <A HREF = "fix_wall_lj93">fix
+for a fix that calculates such a contribution.  For example, the <A HREF = "fix_wall.html">fix
 wall/lj93</A> fix calculates the energy of atoms
 interacting with the wall.  See the doc pages for "individual fixes"
 to see which ones contribute.
--- a/doc/thermo_style.txt
+++ b/doc/thermo_style.txt
@ -176,7 +176,7 @@ components of velocity and/or include different degrees of freedom
 The potential energy of the system {pe} will include contributions
 from fixes if the "fix_modify thermo"_fix_modify.html option is set
 for a fix that calculates such a contribution.  For example, the "fix
-wall/lj93"_fix_wall_lj93 fix calculates the energy of atoms
+wall/lj93"_fix_wall.html fix calculates the energy of atoms
 interacting with the wall.  See the doc pages for "individual fixes"
 to see which ones contribute.
--- a/doc/variable.html
+++ b/doc/variable.html
@ -76,7 +76,7 @@ which when evaluated produces a single numeric value which can be
 output either directly (see the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix
 print</A>, and <A HREF = "run.html">run every</A> commands) or as part
 of thermodynamic output (see the <A HREF = "thermo_style.html">thermo_style</A>
-command), or used as input to an averaging fix (see the <A HREF = "fix_ave/time">fix
+command), or used as input to an averaging fix (see the <A HREF = "fix_ave_time">fix
 ave/time</A> command).  Variables of style <I>atom</I> store a
 formula which when evaluated produces one numeric value per atom which
 can be output to a dump file (see the <A HREF = "dump.html">dump custom</A> command)
@ -328,7 +328,7 @@ return components of the position and velocity of the center of mass
 of the group.  Fcm() returns a component of the total force on the
 group of atoms.  Bound() returns the min/max of a particular
 coordinate for all atoms in the group.  Gyration() computes the
-radius-of-gyration of the group of atoms.  See the <A HREF = "fix_gyration.html">fix
+radius-of-gyration of the group of atoms.  See the <A HREF = "compute_gyration.html">compute
 gyration</A> command for a definition of the formula.
 </P>
 <P>Region functions are exactly the same as group functions except they
--- a/doc/variable.txt
+++ b/doc/variable.txt
@ -71,7 +71,7 @@ output either directly (see the "print"_print.html, "fix
 print"_fix_print.html, and "run every"_run.html commands) or as part
 of thermodynamic output (see the "thermo_style"_thermo_style.html
 command), or used as input to an averaging fix (see the "fix
-ave/time"_fix_ave/time command).  Variables of style {atom} store a
+ave/time"_fix_ave_time command).  Variables of style {atom} store a
 formula which when evaluated produces one numeric value per atom which
 can be output to a dump file (see the "dump custom"_dump.html command)
 or used as input to an averaging fix (see the "fix
@ -323,8 +323,8 @@ return components of the position and velocity of the center of mass
 of the group.  Fcm() returns a component of the total force on the
 group of atoms.  Bound() returns the min/max of a particular
 coordinate for all atoms in the group.  Gyration() computes the
-radius-of-gyration of the group of atoms.  See the "fix
+radius-of-gyration of the group of atoms.  See the "compute
-gyration"_fix_gyration.html command for a definition of the formula.
+gyration"_compute_gyration.html command for a definition of the formula.
 Region functions are exactly the same as group functions except they
 take an extra argument which is the region ID.  The function is