LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-59-g16e0a7788a)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of Gaussian descriptors on a grid
# for a cell with two atoms of type 1 and type 2.
# The output in dump.glocal shows that for grid points
# sitting on an atom of type 1 or 2:
# val1 = 1.0/(0.1355*sqrt(2.0*pi))**3 = 25.5219
# val2 = 1.0/(0.2   *sqrt(2.0*pi))**3 = 7.93670
# These values are extracted to the log file
#

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

units		metal
atom_modify	map hash

# generate the box and atom positions using a BCC lattice

variable       	nx equal ${nrep}
variable       	nx equal 1
variable 	ny equal ${nrep}
variable 	ny equal 1
variable 	nz equal ${nrep}
variable 	nz equal 1

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
lattice		custom 3.316 		a1 1 0 0 		a2 0 1 0  		a3 0 0 1 		basis 0 0 0 		basis 0.5 0.5 0.5
Lattice spacing in x,y,z = 3.316 3.316 3.316
region		box block 0 ${nx} 0 ${ny} 0 ${nz}
region		box block 0 1 0 ${ny} 0 ${nz}
region		box block 0 1 0 1 0 ${nz}
region		box block 0 1 0 1 0 1
create_box	2 box
Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
  1 by 2 by 2 MPI processor grid
create_atoms	1 box basis 1 1 basis 2 2
Created 2 atoms
  using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
  create_atoms CPU = 0.001 seconds

mass 		* 180.88

# define atom compute and grid compute

variable 	rcutfac equal 4.67637
variable 	radelem1 equal 0.5
variable 	radelem2 equal 0.5
variable	sigmaelem1 equal 0.1355
variable	sigmaelem2 equal 0.2
variable 	gaussian_options string 		"${rcutfac} ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}"
4.67637 ${radelem1} ${radelem2} ${sigmaelem1} ${sigmaelem2}
4.67637 0.5 ${radelem2} ${sigmaelem1} ${sigmaelem2}
4.67637 0.5 0.5 ${sigmaelem1} ${sigmaelem2}
4.67637 0.5 0.5 0.1355 ${sigmaelem2}
4.67637 0.5 0.5 0.1355 0.2

# build zero potential to force ghost atom creation

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

# define atom and grid computes

compute 	mygridlocal all gaussian/grid/local grid ${ngrid} ${ngrid} ${ngrid} 	 	${gaussian_options}
compute 	mygridlocal all gaussian/grid/local grid 2 ${ngrid} ${ngrid} 	 	${gaussian_options}
compute 	mygridlocal all gaussian/grid/local grid 2 2 ${ngrid} 	 	${gaussian_options}
compute 	mygridlocal all gaussian/grid/local grid 2 2 2 	 	${gaussian_options}
compute 	mygridlocal all gaussian/grid/local grid 2 2 2 	 	4.67637 0.5 0.5 0.1355 0.2

# define output

dump		1 all local 1000 dump.glocal c_mygridlocal[*]
dump 		2 all custom 1000 dump.gatom id x y z
compute		val1 all reduce max c_mygridlocal[7] inputs local
compute		val2 all reduce max c_mygridlocal[8] inputs local
thermo_style	custom step c_val1 c_val2

# run

run		0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 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 = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair zero, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
Per MPI rank memory allocation (min/avg/max) = 3.522 | 3.523 | 3.524 Mbytes
   Step         c_val1         c_val2    
         0   25.521859      7.9367045    
Loop time of 2.238e-06 on 4 procs for 0 steps with 2 atoms

89.4% 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   |            | 2.238e-06  |            |       |100.00

Nlocal:            0.5 ave           1 max           0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:          274.5 ave         275 max         274 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs:             16 ave          40 max           0 min
Histogram: 2 0 0 0 0 0 1 0 0 1

Total # of neighbors = 64
Ave neighs/atom = 32
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00