Merge branch 'master' into lammps-icms

doc/Eqs/transform.tex

@@ -0,0 +1,17 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\vec{a} &=& (a_x,0,0) \\
+\vec{b} &=& (b_x,b_y,0) \\
+\vec{c} &=& (c_x,c_y,c_z) \\
+a_x &=& A \\
+b_x &=& (\vec{B} \bullet \vec{A}) \,\, / \,\, A \\
+b_y &=& |\vec{A} \times \vec{B}| \,\, / \,\, A \quad \rm{or} \quad  \sqrt{B^2 - {b_x}^2} \\
+c_x &=& (\vec{C} \bullet \vec{A}) \,\, / \,\, A \\
+c_y &=& [\vec{C} \bullet ((\vec{A} \times \vec{B}) \times \vec{A})] \,\, / \,\, |(\vec{A} \times \vec{B}) \times \vec{A}| \quad \rm{or} \quad \sqrt{C^2 - {c_x}^2 -{c_z}^2} \\
+c_z &=& [\vec{C} \bullet (\vec{A} \times \vec{B})] \,\, / \,\, |\vec{A} \times \vec{B}| \\
+\end{eqnarray*}
+
+\end{document}

doc/Section_howto.html

@@ -785,6 +785,15 @@ arbitrary vectors.  As indicated, <B>a</B> must be aligned with the x axis,
 not a restriction since it is possible to rotate any set of 3 crystal
 basis vectors so that they meet this restriction.
 </P>
+<P>For example, assume that the 3 vectors <B>A</B>,<B>B</B>,<B>C</B> are the edge
+vectors of a general parallelipied, where there is no directional
+requirements <B>A</B>,<B>B</B>,<B>C</B> other than they are not co-linear and that
+<B>C</B> dotted into (<B>A</B> x <B>B</B>) be > 0, i.e.  the vectors are ordered to
+satisfy a right-hand rule.  The equivalent LAMMPS <B>a</B>,<B>b</B>,<B>c</B> vectors
+can be computed as follows where A = |<B>A</B>| = scalar length of <B>A</B>.
+</P>
+<CENTER><IMG SRC = "Eqs/transform.jpg">
+</CENTER>
 <P>There is no requirement that a triclinic box be periodic in any
 dimension, though it typically should be in at least the 2nd dimension
 of the tilt (y in xy) if you want to enforce a shift in periodic

doc/Section_howto.txt

@@ -776,6 +776,15 @@ arbitrary vectors.  As indicated, [a] must be aligned with the x axis,
 not a restriction since it is possible to rotate any set of 3 crystal
 basis vectors so that they meet this restriction.
 
+For example, assume that the 3 vectors [A],[B],[C] are the edge
+vectors of a general parallelipied, where there is no directional
+requirements [A],[B],[C] other than they are not co-linear and that
+[C] dotted into ([A] x [B]) be > 0, i.e.  the vectors are ordered to
+satisfy a right-hand rule.  The equivalent LAMMPS [a],[b],[c] vectors
+can be computed as follows where A = |[A]| = scalar length of [A].
+
+:c,image(Eqs/transform.jpg)
+
 There is no requirement that a triclinic box be periodic in any
 dimension, though it typically should be in at least the 2nd dimension
 of the tilt (y in xy) if you want to enforce a shift in periodic

examples/kim/in.kim.lj

@@ -22,7 +22,7 @@ create_atoms	1 box
 #pair_coeff	1 1 0.0031 2.7400
 #pair_modify     shift yes
 
-pair_style      kim model_Ne_P_fastLJ
+pair_style      kim ex+model_Ne_P_fastLJ
 pair_coeff      * * Ne
 
 mass		1 20.18