# 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 1
variable a index 3.316
variable ngrid index 2

units		metal

# 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

region		box block 0 ${nx} 0 ${ny} 0 ${nz}
create_box	1 box
create_atoms	1 box

mass 1 180.88

# 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}

# 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 1000 dump_b id c_b[*]

# run

run 0