Updated compute hexorder/atom, added compute orientorder/atom

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14252 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Eqs/orientorder.tex

@@ -6,7 +6,7 @@ $$
 $$
 
 $$
-   Q^2_l = \frac{4 \pi}{2 l + 1} \sum_{m = -l}^{m = l} \bar{Y}_{lm} \bar{Y}^*_{lm}
+   Q_l = \sqrt{\frac{4 \pi}{2 l + 1} \sum_{m = -l}^{m = l} \bar{Y}_{lm} \bar{Y}^*_{lm}}
    $$
 
 \end{document}

doc/compute_hexorder_atom.html

@@ -21,17 +21,17 @@
 
 <LI>one or more keyword/value pairs may be appended 
 
-<PRE>keyword = <I>n</I> or <I>nnn</I> or <I>cutoff</I> 
+<PRE>keyword = <I>degree</I> or <I>nnn</I> or <I>cutoff</I> 
   <I>cutoff</I> value = distance cutoff
   <I>nnn</I> value = number of nearest neighbors
-  <I>n</I> value = degree of order parameter 
+  <I>degree</I> value = degree <I>n</I> of order parameter 
 </PRE>
 
 </UL>
 <P><B>Examples:</B>
 </P>
 <PRE>compute 1 all hexorder/atom 
-compute 1 all hexorder/atom n 4 nnn 4 cutoff 1.2 
+compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -62,7 +62,7 @@ neighbors used to calculate <I>qn</I>. The default value is 6.
 If the value is NULL, then all neighbors up to the 
 distance cutoff are used.
 </P>
-<P>The optional keyword <I>n</I> sets the degree of the order parameter. 
+<P>The optional keyword <I>degree</I> sets the degree <I>n</I> of the order parameter. 
 The default value is 6. For a perfect hexagonal lattice with 
 <I>nnn</I> = 6,
 <I>q</I>6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 
@@ -114,7 +114,7 @@ options.
 </P>
 <P><B>Default:</B> 
 </P>
-<P>The option defaults are <I>n</I> = 6, <I>nnn</I> = 6, <I>cutoff</I> = pair style cutoff
+<P>The option defaults are <I>cutoff</I> = pair style cutoff, <I>nnn</I> = 6, <I>degree</I> = 6
 </P>
 <HR>
 

doc/compute_hexorder_atom.txt

@@ -15,17 +15,17 @@ compute ID group-ID hexorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 hexorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {n} or {nnn} or {cutoff} 
+keyword = {degree} or {nnn} or {cutoff} 
   {cutoff} value = distance cutoff
   {nnn} value = number of nearest neighbors
-  {n} value = degree of order parameter :pre
+  {degree} value = degree {n} of order parameter :pre
 
 :ule
 
 [Examples:]
 
 compute 1 all hexorder/atom 
-compute 1 all hexorder/atom n 4 nnn 4 cutoff 1.2 :pre
+compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2 :pre
 
 [Description:]
 
@@ -56,7 +56,7 @@ neighbors used to calculate {qn}. The default value is 6.
 If the value is NULL, then all neighbors up to the 
 distance cutoff are used.
 
-The optional keyword {n} sets the degree of the order parameter. 
+The optional keyword {degree} sets the degree {n} of the order parameter. 
 The default value is 6. For a perfect hexagonal lattice with 
 {nnn} = 6,
 {q}6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 
@@ -108,7 +108,7 @@ options.
 
 [Default:] 
 
-The option defaults are {n} = 6, {nnn} = 6, {cutoff} = pair style cutoff
+The option defaults are {cutoff} = pair style cutoff, {nnn} = 6, {degree} = 6
 
 :line
 

doc/compute_orientorder_atom.txt

@@ -45,8 +45,8 @@ The summation is over the {nnn} nearest
 neighbors of the central atom. 
 The angles theta and phi are the standard spherical polar angles 
 defining the direction of the bond vector {rij}.
-The second equation defines the square power of {Ql}, which are 
-rotationally invariant scalar quantities obtained by summing 
+The second equation defines {Ql}, which is a
+rotationally invariant scalar quantity obtained by summing 
 over all the components of degree {l}. 
 
 The optional keyword {cutoff} defines the distance cutoff
@@ -65,7 +65,9 @@ parameters. This is followed by that number of integers giving the
 degree of each order parameter. Because {Q}2 and all odd-degree 
 order parameters are zero for atoms in cubic crystals 
 (see "Steinhardt"_#Steinhardt), the default order parameters
-are {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+are {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. The correct 
+numerical values for commonly encountered high-symmetry 
+structures are given by "Mickel et al."_#Mickel
 
 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than 
@@ -113,3 +115,5 @@ The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5
 
 :link(Steinhardt)
 [(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
+:link(Mickel)
+[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).

src/compute_hexorder_atom.cpp

@@ -56,7 +56,7 @@ ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) :
 
   int iarg = 3;
   while (iarg < narg) {
-    if (strcmp(arg[iarg],"n") == 0) {
+    if (strcmp(arg[iarg],"degree") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal compute hexorder/atom command");
       ndegree = force->numeric(FLERR,arg[iarg+1]);
       if (ndegree < 0)