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rohskopf
2022-07-07 09:11:28 -06:00
parent 581503888f b8acd2e31d
commit 9975eecd2a
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# Demonstrate calculation of SNAP bispectrum descriptors on a grid
# CORRECTNESS: The two atom positions coincide with two of
# the gridpoints, so c_b[2][1-5] should match c_mygrid[8][4-8].
# The same is true for compute grid/local c_mygridlocal[8][4-11].
# Local arrays can not be access directly in the script,
# but they are printed out to file dump.blocal
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 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 &
region box block 0 ${nx} 0 ${ny} 0 ${nz}
create_box 1 box
create_atoms 1 box
mass 1 180.88
# define atom compute and grid compute
group snapgroup type 1
variable twojmax equal 2
variable rcutfac equal 4.67637
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable wj equal 1
variable radelem equal 0.5
variable bzero equal 0
variable quadratic equal 0
variable switch equal 1
variable snap_options string &
"${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 ${ngrid} ${ngrid} ${ngrid} &
${snap_options}
compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} &
${snap_options}
# define output
variable B5atom equal c_b[2][5]
variable B5grid equal c_mygrid[8][8]
variable rmse_global equal "sqrt( &
(c_mygrid[8][1] - x[2])^2 + &
(c_mygrid[8][2] - y[2])^2 + &
(c_mygrid[8][3] - z[2])^2 + &
(c_mygrid[8][4] - c_b[2][1])^2 + &
(c_mygrid[8][5] - c_b[2][2])^2 + &
(c_mygrid[8][6] - c_b[2][3])^2 + &
(c_mygrid[8][7] - c_b[2][4])^2 + &
(c_mygrid[8][8] - c_b[2][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 c_mygridlocal[*]
dump 2 all custom 1000 dump.batom id x y z c_b[*]
# run
run 0

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# 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

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LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of SNAP bispectrum descriptors on a grid
# CORRECTNESS: The two atom positions coincide with two of
# the gridpoints, so c_b[2][1-5] should match c_mygrid[8][4-8].
# The same is true for compute grid/local c_mygridlocal[8][4-11].
# Local arrays can not be access directly in the script,
# but they are printed out to file dump.blocal
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 ${nz}
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 2 atoms
using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
create_atoms CPU = 0.000 seconds
mass 1 180.88
# define atom compute and grid compute
group snapgroup type 1
2 atoms in group snapgroup
variable twojmax equal 2
variable rcutfac equal 4.67637
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable wj equal 1
variable radelem equal 0.5
variable bzero equal 0
variable quadratic equal 0
variable switch equal 1
variable snap_options string "${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 ${ngrid} ${ngrid} ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 ${ngrid} ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 2 ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 2 2 ${snap_options}
compute mygrid all sna/grid grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 ${ngrid} ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 2 ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
# define output
variable B5atom equal c_b[2][5]
variable B5grid equal c_mygrid[8][8]
variable rmse_global equal "sqrt( (c_mygrid[8][1] - x[2])^2 + (c_mygrid[8][2] - y[2])^2 + (c_mygrid[8][3] - z[2])^2 + (c_mygrid[8][4] - c_b[2][1])^2 + (c_mygrid[8][5] - c_b[2][2])^2 + (c_mygrid[8][6] - c_b[2][3])^2 + (c_mygrid[8][7] - c_b[2][4])^2 + (c_mygrid[8][8] - c_b[2][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 c_mygridlocal[*]
dump 2 all custom 1000 dump.batom 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 = 1 1 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
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) = 7.127 | 7.127 | 7.127 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 9.1551336e-16
Loop time of 1.43e-06 on 1 procs for 0 steps with 2 atoms
139.9% CPU use with 1 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 | | 1.43e-06 | | |100.00
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 339 ave 339 max 339 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 128
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (2 Jun 2022)
using 1 OpenMP thread(s) per MPI task
# Demonstrate calculation of SNAP bispectrum descriptors on a grid
# CORRECTNESS: The two atom positions coincide with two of
# the gridpoints, so c_b[2][1-5] should match c_mygrid[8][4-8].
# The same is true for compute grid/local c_mygridlocal[8][4-11].
# Local arrays can not be access directly in the script,
# but they are printed out to file dump.blocal
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 ${nz}
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (3.316 3.316 3.316)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 2 atoms
using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316)
create_atoms CPU = 0.001 seconds
mass 1 180.88
# define atom compute and grid compute
group snapgroup type 1
2 atoms in group snapgroup
variable twojmax equal 2
variable rcutfac equal 4.67637
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable wj equal 1
variable radelem equal 0.5
variable bzero equal 0
variable quadratic equal 0
variable switch equal 1
variable snap_options string "${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 ${ngrid} ${ngrid} ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 ${ngrid} ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 2 ${ngrid} ${snap_options}
compute mygrid all sna/grid grid 2 2 2 ${snap_options}
compute mygrid all sna/grid grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
compute mygridlocal all sna/grid/local grid ${ngrid} ${ngrid} ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 ${ngrid} ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 ${ngrid} ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 2 ${snap_options}
compute mygridlocal all sna/grid/local grid 2 2 2 4.67637 0.99363 2 0.5 1 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 1
# define output
variable B5atom equal c_b[2][5]
variable B5grid equal c_mygrid[8][8]
variable rmse_global equal "sqrt( (c_mygrid[8][1] - x[2])^2 + (c_mygrid[8][2] - y[2])^2 + (c_mygrid[8][3] - z[2])^2 + (c_mygrid[8][4] - c_b[2][1])^2 + (c_mygrid[8][5] - c_b[2][2])^2 + (c_mygrid[8][6] - c_b[2][3])^2 + (c_mygrid[8][7] - c_b[2][4])^2 + (c_mygrid[8][8] - c_b[2][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 c_mygridlocal[*]
dump 2 all custom 1000 dump.batom 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 = 1 1 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
Per MPI rank memory allocation (min/avg/max) = 6.123 | 6.631 | 7.139 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 1.6316879e-15
Loop time of 2.57125e-06 on 4 procs for 0 steps with 2 atoms
107.0% 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 | | 2.571e-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
FullNghs: 32 ave 64 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 128
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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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 ${nz}
region box prism 0 3 0 2 0 1 2 1 1
create_box 1 box
Created triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
WARNING: Triclinic box skew is large (src/domain.cpp:224)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 12 atoms
using lattice units in triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316)
create_atoms CPU = 0.000 seconds
mass 1 180.88
# define atom compute and grid compute
group snapgroup type 1
12 atoms in group snapgroup
variable twojmax equal 2
variable rcutfac equal 4.67637
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable wj equal 1
variable radelem equal 0.5
variable bzero equal 0
variable quadratic equal 0
variable switch equal 1
variable snap_options string "${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) = 7.183 | 7.183 | 7.183 Mbytes
Step v_B5atom v_B5grid v_rmse_global
0 1.0427295 1.0427295 7.2262471e-14
Loop time of 1.414e-06 on 1 procs for 0 steps with 12 atoms
70.7% CPU use with 1 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 | | 1.414e-06 | | |100.00
Nlocal: 12 ave 12 max 12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 604 ave 604 max 604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 768 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 768
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

192
examples/snap/log.15Jun22.grid.tri.g++.4 Normal file
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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