git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8450 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_packages.html

@@ -44,24 +44,24 @@ packages, more details are provided.
 </P>
 <DIV ALIGN=center><TABLE  BORDER=1 >
 <TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR>
-<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">howto</A></TD><TD > ellipse</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">Section_howto</A></TD><TD > ellipse</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >CLASS2</TD><TD > class 2 force fields</TD><TD > -</TD><TD > <A HREF = "pair_class2.html">pair_style lj/class2</A></TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled potentials</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "Section_accelerate.html#acc_3">Section accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
-<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6<A HREF = "pair_kim.html">>howto</A></TD><TD > pour</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">Section_howto</A></TD><TD > pour</TD><TD > -</TD></TR>
-<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > pair_style kim</A></TD><TD > kim</TD><TD > lib/kim</TD></TR>
+<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > <A HREF = "pair_kim.html">pair_style kim</A></TD><TD > kim</TD><TD > lib/kim</TD></TR>
 <TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
 <TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
-<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">howto</A></TD><TD > peptide</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">Section_howto</A></TD><TD > peptide</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >OPT</TD><TD > optimized pair potentials</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "Section_accelerate.html#acc_1">Section accelerate</A></TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >PERI</TD><TD > Peridynamics models</TD><TD > Mike Parks (Sandia)</TD><TD > <A HREF = "pair_peri.html">pair_style peri</A></TD><TD > peri</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >POEMS</TD><TD > coupled rigid body motion</TD><TD > Rudra Mukherjee (JPL)</TD><TD > <A HREF = "fix_poems.html">fix poems</A></TD><TD > rigid</TD><TD > lib/poems</TD></TR>
 <TR ALIGN="center"><TD >REAX</TD><TD > ReaxFF potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_reax.html">pair_style reax</A></TD><TD > reax</TD><TD >  lib/reax</TD></TR>
-<TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">howto</A></TD><TD > tad</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">Section_howto</A></TD><TD > tad</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >SHOCK</TD><TD > shock loading methods</TD><TD > -</TD><TD > <A HREF = "fix_msst.html">fix msst</A></TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >SRD</TD><TD > stochastic rotation dynamics</TD><TD > -</TD><TD > <A HREF = "fix_srd.html">fix srd</A></TD><TD > srd</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >XTC</TD><TD > dumps in XTC format</TD><TD > -</TD><TD > <A HREF = "dump.html">dump</A></TD><TD > -</TD><TD > -</TD></TR>

doc/Section_packages.txt

@@ -39,24 +39,24 @@ packages, more details are provided.
 The current list of standard packages is as follows:
 
 Package, Description, Author(s), Doc page, Example, Library
-ASPHERE, aspherical particles, -, "howto"_Section_howto.html#howto_14, ellipse, -
+ASPHERE, aspherical particles, -, "Section_howto"_Section_howto.html#howto_14, ellipse, -
 CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
 COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, -
 DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
 FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, -
 GPU, GPU-enabled potentials, Mike Brown (ORNL), "Section accelerate"_Section_accelerate.html#acc_3, gpu, lib/gpu
-GRANULAR, granular systems, -, "howto"_Section_howto.html#howto_6, pour, -
+GRANULAR, granular systems, -, "Section_howto"_Section_howto.html#howto_6, pour, -
-KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), pair_style kim"_pair_kim.html, kim, lib/kim
+KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, lib/kim
 KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
 MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
 MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
 MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
-MOLECULE, molecular system force fields, -, "howto"_Section_howto.html#howto_3, peptide, -
+MOLECULE, molecular system force fields, -, "Section_howto"_Section_howto.html#howto_3, peptide, -
 OPT, optimized pair potentials, Fischer & Richie & Natoli (2), "Section accelerate"_Section_accelerate.html#acc_1, -, -
 PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
 POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
 REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax
-REPLICA, multi-replica methods, -, "howto"_Section_howto.html#howto_5, tad, -
+REPLICA, multi-replica methods, -, "Section_howto"_Section_howto.html#howto_5, tad, -
 SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
 SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
 XTC, dumps in XTC format, -, "dump"_dump.html, -, -

doc/min_modify.html

@@ -20,7 +20,7 @@
 <PRE>keyword = <I>dmax</I> or <I>line</I>
   <I>dmax</I> value = max
     max = maximum distance for line search to move (distance units)
-  <I>line</I> value = <I>backtrack</I> or <I>quadratic</I>or <I>forcezero</I>
+  <I>line</I> value = <I>backtrack</I> or <I>quadratic</I> or <I>forcezero</I>
     backtrack,quadratic,forcezero = style of linesearch to use 
 </PRE>
 

doc/min_modify.txt

@@ -16,7 +16,7 @@ one or more keyword/value pairs may be listed :ulb,l
 keyword = {dmax} or {line}
   {dmax} value = max
     max = maximum distance for line search to move (distance units)
-  {line} value = {backtrack} or {quadratic}or {forcezero}
+  {line} value = {backtrack} or {quadratic} or {forcezero}
     backtrack,quadratic,forcezero = style of linesearch to use :pre
 :ule