From f44470fe637a3e87d230c077c44010f00ced534b Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Fri, 23 Aug 2019 16:28:13 -0600 Subject: [PATCH] Added fcc and bcc examples for the Steinhardt-Nelson parameters --- doc/src/compute_orientorder_atom.txt | 4 +-- src/steinhardt/in.bcc | 47 ++++++++++++++++++++++++++++ src/steinhardt/in.fcc | 39 +++++++++++++++++++++++ 3 files changed, 88 insertions(+), 2 deletions(-) create mode 100644 src/steinhardt/in.bcc create mode 100644 src/steinhardt/in.fcc diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt index 7327a7b1d3..2e83f3ea07 100644 --- a/doc/src/compute_orientorder_atom.txt +++ b/doc/src/compute_orientorder_atom.txt @@ -27,7 +27,7 @@ keyword = {cutoff} or {nnn} or {degrees} or {components} compute 1 all orientorder/atom compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 -compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre +compute 1 all orientorder/atom degrees 2 4 6 components 6 nnn NULL cutoff 3.0 :pre [Description:] @@ -48,7 +48,7 @@ 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 {Ql}, which is a -rotationally invariant scalar quantity obtained by summing +rotationally invariant non-negative amplitude obtained by summing over all the components of degree {l}. The optional keyword {cutoff} defines the distance cutoff diff --git a/src/steinhardt/in.bcc b/src/steinhardt/in.bcc new file mode 100644 index 0000000000..acdfca3647 --- /dev/null +++ b/src/steinhardt/in.bcc @@ -0,0 +1,47 @@ +# Steinhardt-Nelson bond orientational order parameters for BCC + +variable rcut equal 3.0 + +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice bcc 1.0 +region box block 0 3 0 3 0 3 +create_box 1 box +create_atoms 1 box + +mass 1 1.0 + +# LJ potentials + +pair_style lj/cut ${rcut} +pair_coeff * * 1.0 1.0 ${rcut} + +# initial velocities + +velocity all create 5.0 482748 +fix 1 all nve + +# 8 neighbors, perfect crystal + +compute qn all orientorder/atom degrees 5 4 6 8 10 12 nnn 8 +compute avqn all reduce ave c_qn[*] + +thermo_style custom step temp epair etotal c_avqn[*] + +run 0 + +# 14 neighbors, perfect crystal dynamically melting + +uncompute qn +compute qn all orientorder/atom degrees 5 4 6 8 10 12 nnn 14 + +timestep 0.003 +thermo 1 + +run 20 diff --git a/src/steinhardt/in.fcc b/src/steinhardt/in.fcc new file mode 100644 index 0000000000..6c6a919d7b --- /dev/null +++ b/src/steinhardt/in.fcc @@ -0,0 +1,39 @@ +# Steinhardt-Nelson bond orientational order parameters for FCC + +variable rcut equal 3.0 + +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice fcc 1.0 +region box block 0 3 0 3 0 3 +create_box 1 box +create_atoms 1 box + +mass 1 1.0 + +# LJ potentials + +pair_style lj/cut ${rcut} +pair_coeff * * 1.0 1.0 ${rcut} + +# initial velocities + +velocity all create 5.0 482748 +fix 1 all nve + +# 12 neighbors, perfect crystal dynamically melting + +compute qn all orientorder/atom # degrees 5 4 6 8 10 12 nnn 12 +compute avqn all reduce ave c_qn[*] + +timestep 0.003 +thermo_style custom step temp epair etotal c_avqn[*] +thermo 1 + +run 20