diff --git a/doc/Eqs/hexorder.jpg b/doc/Eqs/hexorder.jpg index 919a4088d0..dafa25cabe 100644 Binary files a/doc/Eqs/hexorder.jpg and b/doc/Eqs/hexorder.jpg differ diff --git a/doc/Eqs/orientorder.jpg b/doc/Eqs/orientorder.jpg index 1c8b5b7dc4..5ec79964f0 100644 Binary files a/doc/Eqs/orientorder.jpg and b/doc/Eqs/orientorder.jpg differ diff --git a/doc/Eqs/orientorder.tex b/doc/Eqs/orientorder.tex index 57844f9365..a081a9eec3 100644 --- a/doc/Eqs/orientorder.tex +++ b/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} diff --git a/doc/compute_hexorder_atom.html b/doc/compute_hexorder_atom.html index 0430fe3ef3..344d1c7a7f 100644 --- a/doc/compute_hexorder_atom.html +++ b/doc/compute_hexorder_atom.html @@ -21,17 +21,17 @@
  • one or more keyword/value pairs may be appended -
    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 
    +  degree value = degree n of order parameter 
     

    Examples:

    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 
     

    Description:

    @@ -62,7 +62,7 @@ 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, q6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 @@ -114,7 +114,7 @@ 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


    diff --git a/doc/compute_hexorder_atom.txt b/doc/compute_hexorder_atom.txt index 65ca7048fa..e1b3779d50 100644 --- a/doc/compute_hexorder_atom.txt +++ b/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 diff --git a/doc/compute_orientorder_atom.txt b/doc/compute_orientorder_atom.txt index 968ee6da20..68d6361b42 100644 --- a/doc/compute_orientorder_atom.txt +++ b/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). diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp index 8027261cb3..eba3c41684 100644 --- a/src/compute_hexorder_atom.cpp +++ b/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)