106 lines
2.9 KiB
Plaintext
106 lines
2.9 KiB
Plaintext
# Demonstrate bispectrum computes
|
|
|
|
# CORRECTNESS: thermo output for c_mygrid[*][1] and c_mygrid[*][8] should
|
|
# match the values in dump_b: 108.173 3.21778 0.712238 7.06634 1.04273
|
|
|
|
# Initialize simulation
|
|
|
|
variable nsteps index 0
|
|
variable nrep index 3
|
|
variable a index 3.316
|
|
variable ngrid index 2
|
|
|
|
units metal
|
|
|
|
atom_modify map yes
|
|
|
|
# generate the box and atom positions using a BCC lattice
|
|
|
|
variable nx equal ${nrep}
|
|
variable ny equal ${nrep}
|
|
variable nz equal ${nrep}
|
|
|
|
boundary p p p
|
|
|
|
lattice custom $a &
|
|
a1 1 0 0 &
|
|
a2 0 1 0 &
|
|
a3 0 0 1 &
|
|
basis 0 0 0 &
|
|
basis 0.5 0.5 0.5 &
|
|
# origin 0.25 0.25 0.25
|
|
# origin 0.25e-3 0.25e-3 0.25e-3
|
|
|
|
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
|
create_box 1 box
|
|
create_atoms 1 box
|
|
|
|
mass 1 180.88
|
|
|
|
write_dump all custom test.dump id type x y z
|
|
|
|
# choose potential
|
|
|
|
include Ta06A.snap
|
|
|
|
# define grid compute and atom compute
|
|
|
|
group snapgroup type 1
|
|
variable twojmax equal 2
|
|
variable rcutfac equal 4.67637
|
|
variable rfac0 equal 0.99363
|
|
variable rmin0 equal 0
|
|
variable wj equal 1
|
|
variable radelem equal 0.5
|
|
variable bzero equal 0
|
|
variable quad equal 0
|
|
variable switch equal 1
|
|
|
|
compute b all sna/atom &
|
|
${rcutfac} ${rfac0} ${twojmax} ${radelem} &
|
|
${wj} rmin0 ${rmin0} bzeroflag ${bzero} &
|
|
quadraticflag ${quad} switchflag ${switch}
|
|
|
|
compute mygrid all sna/grid grid ${ngrid} ${ngrid} ${ngrid} &
|
|
${rcutfac} ${rfac0} ${twojmax} ${radelem} &
|
|
${wj} rmin0 ${rmin0} bzeroflag ${bzero} &
|
|
quadraticflag ${quad} switchflag ${switch}
|
|
|
|
compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} &
|
|
${rcutfac} ${rfac0} ${twojmax} ${radelem} &
|
|
${wj} rmin0 ${rmin0} bzeroflag ${bzero} &
|
|
quadraticflag ${quad} switchflag ${switch}
|
|
|
|
# define output
|
|
|
|
# mygrid is ngrid by (3+nbis) = 8x8
|
|
thermo_style custom step temp ke pe vol &
|
|
c_mygrid[1][1] c_mygrid[2][1] c_mygrid[3][1] c_mygrid[4][1] c_mygrid[5][1] c_mygrid[6][1] c_mygrid[7][1] c_mygrid[8][1] &
|
|
c_mygrid[1][2] c_mygrid[2][2] c_mygrid[3][2] c_mygrid[4][2] c_mygrid[5][2] c_mygrid[6][2] c_mygrid[7][2] c_mygrid[8][2] &
|
|
c_mygrid[1][3] c_mygrid[2][3] c_mygrid[3][3] c_mygrid[4][3] c_mygrid[5][3] c_mygrid[6][3] c_mygrid[7][3] c_mygrid[8][3] &
|
|
c_mygrid[1][4] c_mygrid[2][4] c_mygrid[3][4] c_mygrid[4][4] c_mygrid[5][4] c_mygrid[6][4] c_mygrid[7][4] c_mygrid[8][4] &
|
|
c_mygrid[1][5] c_mygrid[2][5] c_mygrid[3][5] c_mygrid[4][5] c_mygrid[5][5] c_mygrid[6][5] c_mygrid[7][5] c_mygrid[8][5] &
|
|
c_mygrid[1][6] c_mygrid[2][6] c_mygrid[3][6] c_mygrid[4][6] c_mygrid[5][6] c_mygrid[6][6] c_mygrid[7][6] c_mygrid[8][6] &
|
|
c_mygrid[1][7] c_mygrid[2][7] c_mygrid[3][7] c_mygrid[4][7] c_mygrid[5][7] c_mygrid[6][7] c_mygrid[7][7] c_mygrid[8][7] &
|
|
c_mygrid[1][8] c_mygrid[2][8] c_mygrid[3][8] c_mygrid[4][8] c_mygrid[5][8] c_mygrid[6][8] c_mygrid[7][8] c_mygrid[8][8]
|
|
thermo_modify norm yes
|
|
|
|
#dump mydump_b all custom 1 dump_b id c_b[*]
|
|
dump mydump_bgridlocal all local 1 dump_bgridlocal index c_mygridlocal[*]
|
|
|
|
# run
|
|
|
|
run 1
|
|
|
|
# rcb
|
|
|
|
comm_style tiled
|
|
balance 0.99 rcb
|
|
run 1
|
|
|
|
# rcb again
|
|
|
|
balance 0.99 rcb
|
|
run 1
|
|
|