Correctly reproduced examples/in.snap.compute, not yet for quadratic case

# Demonstrate MLIAP quadratic compute

# initialize simulation

variable 	nsteps index 0

variable 	nrep equal 1

variable 	a equal 2.0

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

atom_modify	map hash

lattice         bcc $a

region		box block 0 ${nx} 0 ${ny} 0 ${nz}

create_box	2 box

create_atoms	2 box

mass 		* 180.88

displace_atoms 	all random 0.1 0.1 0.1 123456

# set up reference potential

variable 	zblcutinner equal 4

variable 	zblcutouter equal 4.8

variable 	zblz equal 73

pair_style 	zbl ${zblcutinner} ${zblcutouter}

pair_coeff 	* * ${zblz} ${zblz}

# choose SNA parameters

variable 	twojmax equal 2

variable 	rcutfac equal 1.0

variable 	rfac0 equal 0.99363

variable 	rmin0 equal 0

variable 	radelem1 equal 2.3

variable 	radelem2 equal 2.0

variable	wj1 equal 1.0

variable	wj2 equal 0.96

variable	quadratic equal 1

variable	bzero equal 0

variable	switch equal 0

variable 	snap_options string &

"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"

# set up per-atom computes

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

group 		snapgroup1 type 1

group 		snapgroup2 type 2

compute         bsum1 snapgroup1 reduce sum c_b[*]

compute         bsum2 snapgroup2 reduce sum c_b[*]

# fix 		bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector

# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector

compute		vbsum all reduce sum c_vb[*]

# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector

variable	db_2_100 equal c_db[2][100]

# set up compute snap generating global array

compute   	snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector

thermo 		100

# test output:   1: total potential energy

#                2: xy component of stress tensor

#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2) 

#                4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j) 

#                5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)

#

#                followed by 5 counterparts from compute snap

thermo_style	custom &

		pe            pxy            c_bsum2[20]   c_vbsum[220]    v_db_2_100 &

		c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][37] 

thermo_modify 	norm no

# dump 		mydump_db all custom 1000 dump_db id c_db[*]

# dump_modify 	mydump_db sort id

# Run MD

run             ${nsteps}

# fix 		bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector

compute		vbsum all reduce sum c_vb[*]

# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector

variable	db_2_30 equal c_db[2][30]

variable	db_2_25 equal c_db[2][25]

# set up compute snap generating global array

# test output:   1: total potential energy

#                2: xy component of stress tensor

#                3: Sum(B_{000}^i, all i of type 2) 

#                4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)

#                5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)

#                4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)

#                5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)

#

#                followed by 5 counterparts from compute snap

thermo_style	custom &

		pe            pxy            c_bsum2[1]   c_vbsum[60]    v_db_2_30 &

		c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[13][12] c_snap[7][12] 

		pe            pxy            c_bsum2[1]   c_vbsum[55]    v_db_2_25 &

		c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12] 

thermo_modify 	norm no

# dump 		mydump_db all custom 1000 dump_db id c_db[*]