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Finished documentation and example

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This commit is contained in:
Aidan Thompson
2019-11-19 00:12:57 -07:00
parent b092a9fffa
commit 921d0794bb
2 changed files with 59 additions and 14 deletions
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21
examples/snap/in.snap.compute
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@ -1,6 +1,6 @@
# Demonstrate bispectrum computes
# Initialize simulation
# initialize simulation
variable nsteps index 0
variable nrep equal 1
@ -35,14 +35,15 @@ variable radelem1 equal 2.3
variable radelem2 equal 2.0
variable wj1 equal 1.0
variable wj2 equal 0.96
variable snap_options string &
"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0"
# Setup dummy potential to satisfy cutoff
# set up dummy potential to satisfy cutoff
pair_style zero ${rcutfac}
pair_coeff * *
# Setup reference potential
# set up reference potential
variable zblcutinner equal 4
variable zblcutouter equal 4.8
@ -50,11 +51,11 @@ variable zblz equal 73
pair_style zbl ${zblcutinner} ${zblcutouter}
pair_coeff * * ${zblz} ${zblz}
# set up old-style per-atom computes
# set up per-atom computes
compute b all sna/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
compute vb all snav/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
compute db all snad/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
compute b all sna/atom ${snap_options}
compute vb all snav/atom ${snap_options}
compute db all snad/atom ${snap_options}
# perform sums over atoms
@ -67,9 +68,9 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
compute vbsum all reduce sum c_vb[*]
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
# set up new-style global compute
# set up compute snap generating global array
compute snap all snap ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
compute snap all snap ${snap_options}
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
thermo 100