diff -Naur lammps-29Sep09/doc/pair_meam.html lammps-12Oct09/doc/pair_meam.html
--- lammps-29Sep09/doc/pair_meam.html	2009-03-24 14:05:27.000000000 -0600
+++ lammps-12Oct09/doc/pair_meam.html	2009-09-30 08:15:27.000000000 -0600
@@ -267,7 +267,7 @@
 <A NAME = "Gullet"></A>
 
 <P><B>(Gullet)</B> Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
-This report may be accessed on-line via <A HREF = "http://www.prod.sandia.gov/cgi-bin/techlib/access-control.pl/2003/038782.pdf">this link</A>.
+This report may be accessed on-line via <A HREF = "http://infoserve.sandia.gov/sand_doc/2003/038782.pdf">this link</A>.
 </P>
 
 
diff -Naur lammps-29Sep09/doc/pair_meam.txt lammps-12Oct09/doc/pair_meam.txt
--- lammps-29Sep09/doc/pair_meam.txt	2009-03-18 16:29:16.000000000 -0600
+++ lammps-12Oct09/doc/pair_meam.txt	2009-09-30 08:15:27.000000000 -0600
@@ -264,7 +264,7 @@
 [(Gullet)] Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
 This report may be accessed on-line via "this link"_sandreport.
 
-:link(sandreport,http://www.prod.sandia.gov/cgi-bin/techlib/access-control.pl/2003/038782.pdf)
+:link(sandreport,http://infoserve.sandia.gov/sand_doc/2003/038782.pdf)
 
 :link(Lee)
 [(Lee)] Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).
@@ -274,4 +274,3 @@
 
 :link(Valone)
 [(Valone)] Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
-
diff -Naur lammps-29Sep09/doc/read_data.txt lammps-12Oct09/doc/read_data.txt
--- lammps-29Sep09/doc/read_data.txt	2009-06-26 12:22:33.000000000 -0600
+++ lammps-12Oct09/doc/read_data.txt	2009-10-02 11:58:12.000000000 -0600
@@ -1,7 +1,9 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Section_commands.html#comm)
+
 :line
 
 read_data command :h3
diff -Naur lammps-29Sep09/src/region_cylinder.cpp lammps-12Oct09/src/region_cylinder.cpp
--- lammps-29Sep09/src/region_cylinder.cpp	2007-08-07 07:44:22.000000000 -0600
+++ lammps-12Oct09/src/region_cylinder.cpp	2009-10-02 11:58:29.000000000 -0600
@@ -79,7 +79,7 @@
     }
     if (axis == 'y') {
       if (strcmp(arg[7],"INF") == 0) hi = BIG;
-      if (domain->triclinic == 0) hi = domain->boxhi[1];
+      else if (domain->triclinic == 0) hi = domain->boxhi[1];
       else hi = domain->boxhi_bound[1];
     }
     if (axis == 'z') {
diff -Naur lammps-29Sep09/tools/pymol_asphere/src/cartesian.cpp lammps-12Oct09/tools/pymol_asphere/src/cartesian.cpp
--- lammps-29Sep09/tools/pymol_asphere/src/cartesian.cpp	2008-01-17 10:11:02.000000000 -0700
+++ lammps-12Oct09/tools/pymol_asphere/src/cartesian.cpp	2009-10-12 09:12:12.000000000 -0600
@@ -18,36 +18,6 @@
 
 #include "cartesian.h"
 
-template class TwoD<double>;
-template class TwoD<float>;
-template class TwoD<unsigned>;
-template ostream & operator<< <double>(ostream &out, const TwoD<double> &t);
-template ostream & operator<< <float>(ostream &out, const TwoD<float> &t);
-template istream & operator>> <double>(istream &in, TwoD<double> &t);
-template istream & operator>> <float>(istream &in, TwoD<float> &t);
-template class ThreeD<int>;
-template class ThreeD<float>;
-template class ThreeD<double>;
-template class ThreeD<unsigned>;
-template ostream & operator<< <float>(ostream &out, const ThreeD<float> &t);
-template istream & operator>> <float>(istream &in, ThreeD<float> &t);
-template ostream & operator<< <double>(ostream &out, const ThreeD<double> &t);
-template istream & operator>> <double>(istream &in, ThreeD<double> &t);
-template ostream & operator<< <unsigned>(ostream &out, const ThreeD<unsigned> &t);
-template istream & operator>> <unsigned>(istream &in, ThreeD<unsigned> &t);
-template ThreeD<unsigned> operator+ (const unsigned one,
-																		 const ThreeD<unsigned> &two);
-template ThreeD<double> operator+(const double one, const ThreeD<double> &two);
-template ThreeD<unsigned> operator- (const unsigned one,
-																		 const ThreeD<unsigned> &two);
-template ThreeD<double> operator-(const double one, const ThreeD<double> &two);
-template ThreeD<unsigned> operator* (const unsigned one,
-																		 const ThreeD<unsigned> &two);
-template ThreeD<double> operator*(const double one, const ThreeD<double> &two);
-template ThreeD<unsigned> operator/ (const unsigned one,
-																		 const ThreeD<unsigned> &two);
-template ThreeD<double> operator/(const double one, const ThreeD<double> &two);
-
 
 // ------------------------ TwoD Stuff
 
@@ -1044,4 +1014,34 @@
   return average/vec.size();
 }
 
+template class TwoD<double>;
+template class TwoD<float>;
+template class TwoD<unsigned>;
+template ostream & operator<< <double>(ostream &out, const TwoD<double> &t);
+template ostream & operator<< <float>(ostream &out, const TwoD<float> &t);
+template istream & operator>> <double>(istream &in, TwoD<double> &t);
+template istream & operator>> <float>(istream &in, TwoD<float> &t);
+template class ThreeD<int>;
+template class ThreeD<float>;
+template class ThreeD<double>;
+template class ThreeD<unsigned>;
+template ostream & operator<< <float>(ostream &out, const ThreeD<float> &t);
+template istream & operator>> <float>(istream &in, ThreeD<float> &t);
+template ostream & operator<< <double>(ostream &out, const ThreeD<double> &t);
+template istream & operator>> <double>(istream &in, ThreeD<double> &t);
+template ostream & operator<< <unsigned>(ostream &out, const ThreeD<unsigned> &t);
+template istream & operator>> <unsigned>(istream &in, ThreeD<unsigned> &t);
+template ThreeD<unsigned> operator+ (const unsigned one,
+																		 const ThreeD<unsigned> &two);
+template ThreeD<double> operator+(const double one, const ThreeD<double> &two);
+template ThreeD<unsigned> operator- (const unsigned one,
+																		 const ThreeD<unsigned> &two);
+template ThreeD<double> operator-(const double one, const ThreeD<double> &two);
+template ThreeD<unsigned> operator* (const unsigned one,
+																		 const ThreeD<unsigned> &two);
+template ThreeD<double> operator*(const double one, const ThreeD<double> &two);
+template ThreeD<unsigned> operator/ (const unsigned one,
+																		 const ThreeD<unsigned> &two);
+template ThreeD<double> operator/(const double one, const ThreeD<double> &two);
+
 
diff -Naur lammps-29Sep09/tools/pymol_asphere/src/spherical.cpp lammps-12Oct09/tools/pymol_asphere/src/spherical.cpp
--- lammps-29Sep09/tools/pymol_asphere/src/spherical.cpp	2007-06-21 16:53:58.000000000 -0600
+++ lammps-12Oct09/tools/pymol_asphere/src/spherical.cpp	2009-10-12 09:12:12.000000000 -0600
@@ -17,13 +17,6 @@
 
 #include "spherical.h"
 
-template class Ball<double>;
-template class Ball<float>;
-template ostream & operator<< <double>(ostream &out, const Ball<double> &t);
-template ostream & operator<< <float>(ostream &out, const Ball<float> &t);
-template istream & operator>> <double>(istream &in, Ball<double> &t);
-template istream & operator>> <float>(istream &in, Ball<float> &t);
-
 // Empty construct. Not necessarily initialized to [0 0]
 template<class numtyp>
 Ball<numtyp>::Ball() {
@@ -143,3 +136,12 @@
 bool Ball<numtyp>::check_bounds(numtyp min,numtyp max) {
   return true;
 }
+
+template class Ball<double>;
+template class Ball<float>;
+template ostream & operator<< <double>(ostream &out, const Ball<double> &t);
+template ostream & operator<< <float>(ostream &out, const Ball<float> &t);
+template istream & operator>> <double>(istream &in, Ball<double> &t);
+template istream & operator>> <float>(istream &in, Ball<float> &t);
+
+