LAMMPS (2 Jun 2022)
  using 1 OpenMP thread(s) per MPI task
# 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*${nrep}
variable     	nrepx equal 3*1
variable     	nrepy equal 2*${nrep}
variable     	nrepy equal 2*1
variable     	nrepz equal 1*${nrep}
variable     	nrepz equal 1*1

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

units	     	metal
atom_modify  	map hash sort 0 0

# generate the box and atom positions using a BCC lattice

variable     	nx equal ${nrepx}
variable     	nx equal 3
variable     	ny equal ${nrepy}
variable     	ny equal 2
variable     	nz equal ${nrepz}
variable     	nz equal 1

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
lattice		custom 3.316 		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
Lattice spacing in x,y,z = 3.316 3.316 3.316

box 		tilt large
region		box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
region		box prism 0 3 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
region		box prism 0 3 0 2 0 ${nz} ${ny} ${nz} ${nz}
region		box prism 0 3 0 2 0 1 ${ny} ${nz} ${nz}
region		box prism 0 3 0 2 0 1 2 ${nz} ${nz}
region		box prism 0 3 0 2 0 1 2 1 ${nz}
region		box prism 0 3 0 2 0 1 2 1 1
create_box	1 box
Created triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
WARNING: Triclinic box skew is large (src/domain.cpp:224)
  2 by 2 by 1 MPI processor grid
create_atoms	1 box
Created 12 atoms
  using lattice units in triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
  create_atoms CPU = 0.000 seconds

mass 		1 180.88

# define atom compute and grid compute

group 		snapgroup type 1
12 atoms in group snapgroup
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}"
4.67637 ${rfac0} ${twojmax} ${radelem} 		${wj} rmin0 ${rmin0} quadraticflag ${quadratic} 		bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 ${twojmax} ${radelem} 		${wj} rmin0 ${rmin0} quadraticflag ${quadratic} 		bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 ${radelem} 		${wj} rmin0 ${rmin0} quadraticflag ${quadratic} 		bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 		${wj} rmin0 ${rmin0} quadraticflag ${quadratic} 		bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 		1 rmin0 ${rmin0} quadraticflag ${quadratic} 		bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 		1 rmin0 0 quadraticflag ${quadratic} 		bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 		1 rmin0 0 quadraticflag 0 		bzeroflag ${bzero} switchflag ${switch}
4.67637 0.99363 2 0.5 		1 rmin0 0 quadraticflag 0 		bzeroflag 0 switchflag ${switch}
4.67637 0.99363 2 0.5 		1 rmin0 0 quadraticflag 0 		bzeroflag 0 switchflag 1

# build zero potential to satisfy compute sna/atom

pair_style      zero ${rcutfac}
pair_style      zero 4.67637
pair_coeff      * *

# define atom and grid computes

compute       	b all sna/atom ${snap_options}
compute       	b all sna/atom 4.67637 0.99363 2 0.5 		1 rmin0 0 quadraticflag 0 		bzeroflag 0 switchflag 1
compute 	mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} 	 	${snap_options}
compute 	mygrid all sna/grid grid 6 ${ngridy} ${ngridz} 	 	${snap_options}
compute 	mygrid all sna/grid grid 6 4 ${ngridz} 	 	${snap_options}
compute 	mygrid all sna/grid grid 6 4 2 	 	${snap_options}
compute 	mygrid all sna/grid grid 6 4 2 	 	4.67637 0.99363 2 0.5 		1 rmin0 0 quadraticflag 0 		bzeroflag 0 switchflag 1
compute 	mygridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} 	 	${snap_options}
compute 	mygridlocal all sna/grid/local grid 6 ${ngridy} ${ngridz} 	 	${snap_options}
compute 	mygridlocal all sna/grid/local grid 6 4 ${ngridz} 	 	${snap_options}
compute 	mygridlocal all sna/grid/local grid 6 4 2 	 	${snap_options}
compute 	mygridlocal all sna/grid/local grid 6 4 2 	 	4.67637 0.99363 2 0.5 		1 rmin0 0 quadraticflag 0 		bzeroflag 0 switchflag 1

# 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
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.67637
  ghost atom cutoff = 6.67637
  binsize = 3.338185, bins = 6 3 1
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair zero, perpetual
      attributes: half, newton on
      pair build: half/bin/newton/tri
      stencil: half/bin/3d/tri
      bin: standard
  (2) compute sna/atom, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.15 | 7.15 | 7.15 Mbytes
   Step        v_B5atom       v_B5grid    v_rmse_global 
         0   1.0427295      1.0427295      1.9367585e-14
Loop time of 2.65825e-06 on 4 procs for 0 steps with 12 atoms

84.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0          | 0          | 0          |   0.0 |  0.00
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 2.658e-06  |            |       |100.00

Nlocal:              3 ave           4 max           2 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:            459 ave         460 max         458 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs:             96 ave         128 max          64 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs:          192 ave         256 max         128 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 768
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0

Total wall time: 0:00:00
