# Demonstrate calculation of SNAP bispectrum
# descriptors on a grid for triclinic cell

# This triclinic cell has 6 times the volume of the single
# unit cell used by in.grid
# and contains 12 atoms.  It is a 3x2x1 supercell
# with each unit cell containing 2 atoms and the
# reduced lattice vectors are [1 0 0], [1 1 0], and [1 1 1].
# The grid is listed in x-fastest order

# CORRECTNESS: The atom positions coincide with certain
# gridpoints, so c_b[1][1-5] should match c_mygrid[1][4-8]
# and c_b[7][1-5] should match c_mygrid[13][4-8].
# Local arrays can not be access directly in the script,
# but they are printed out to file dump.blocal.tri

# Initialize simulation

variable     	nrep index 1
variable     	a index 3.316
variable     	ngrid index 2

variable     	nrepx equal 3*${nrep}
variable     	nrepy equal 2*${nrep}
variable     	nrepz equal 1*${nrep}

variable     	ngridx equal 3*${ngrid}
variable     	ngridy equal 2*${ngrid}
variable     	ngridz equal 1*${ngrid}

units	     	metal
atom_modify  	map hash sort 0 0

# generate the box and atom positions using a BCC lattice

variable     	nx equal ${nrepx}
variable     	ny equal ${nrepy}
variable     	nz equal ${nrepz}

boundary     	p p p

lattice		custom $a &
		a1 1 0 0 &
		a2 1 1 0  &
		a3 1 1 1 &
		basis 0 0 0 &
		basis 0.0 0.0 0.5 &
		spacing 1 1 1

box 		tilt large
region		box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
create_box	1 box
create_atoms	1 box

mass 		1 180.88

# define atom compute and grid 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 	quadratic equal 0
variable 	switch equal 1

variable 	snap_options string &
		"${rcutfac} ${rfac0} ${twojmax} ${radelem} &
		${wj} rmin0 ${rmin0} quadraticflag ${quadratic} &
		bzeroflag ${bzero} switchflag ${switch}"

# build zero potential to satisfy compute sna/atom

pair_style      zero ${rcutfac}
pair_coeff      * *

# define atom and grid computes

compute       	b all sna/atom ${snap_options}
compute 	mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} &
	 	${snap_options}
compute 	mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} &
	 	${snap_options}

# define output

variable	B5atom equal c_b[7][5]
variable	B5grid equal c_mygrid[13][8]

# do not compare x,y,z because assignment of ids
# to atoms is not unnique for different processor grids

variable	rmse_global equal "sqrt(    &
	 (c_mygrid[13][4] - c_b[7][1])^2 + &
	 (c_mygrid[13][5] - c_b[7][2])^2 + &
	 (c_mygrid[13][6] - c_b[7][3])^2 + &
	 (c_mygrid[13][7] - c_b[7][4])^2 + &
	 (c_mygrid[13][8] - c_b[7][5])^2   &
	 )"

thermo_style	custom step v_B5atom v_B5grid v_rmse_global

# this is the only way to view the local grid

dump 1 all local 1000 dump.blocal.tri c_mygridlocal[*]
dump 2 all custom 1000 dump.batom.tri id x y z c_b[*]

# run

run		0