lammps/examples/mliap/log.03Jul20.mliap.snap.comp...

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Groff

LAMMPS (30 Jun 2020)
# Demonstrate bispectrum computes
# 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 nx equal 1
variable ny equal ${nrep}
variable ny equal 1
variable nz equal ${nrep}
variable nz equal 1
boundary p p p
atom_modify map hash
lattice bcc $a
lattice bcc 2
Lattice spacing in x,y,z = 2 2 2
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 (2 2 2)
1 by 1 by 1 MPI processor grid
create_atoms 2 box
Created 2 atoms
create_atoms CPU = 0.000 seconds
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_style zbl 4 ${zblcutouter}
pair_style zbl 4 4.8
pair_coeff * * ${zblz} ${zblz}
pair_coeff * * 73 ${zblz}
pair_coeff * * 73 73
# choose SNA parameters
variable twojmax equal 2
variable rcutfac equal 1.0
variable rfac0 equal 0.99363
variable rmin0 equal 0
variable radelem1 equal 2.3
variable radelem2 equal 2.0
variable wj1 equal 1.0
variable wj2 equal 0.96
variable quadratic equal 0
variable bzero equal 0
variable switch equal 0
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
# set up per-atom computes
compute b all sna/atom ${snap_options}
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
compute vb all snav/atom ${snap_options}
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
compute db all snad/atom ${snap_options}
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
# perform sums over atoms
group snapgroup1 type 1
0 atoms in group snapgroup1
group snapgroup2 type 2
2 atoms in group snapgroup2
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_25 equal c_db[2][25]
thermo 100
# test output: 1: total potential energy
# 2: xy component of stress tensor
# 3: Sum(B_{000}^i, 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
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 1
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
SNAP keyword elems A
SNAP keyword radelems 2.3
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector
thermo_style custom 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
run ${nsteps}
run 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 1 1 1
5 neighbor lists, perpetual/occasional/extra = 1 4 0
(1) pair zbl, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute snav/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute snad/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(5) compute mliap, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.75 | 10.75 | 10.75 Mbytes
PotEng 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]
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
Loop time of 0 on 1 procs for 0 steps with 2 atoms
0.0% CPU use with 1 MPI tasks x no 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 | | 0 | | | 0.00
Nlocal: 2.0 ave 2.0 max 2.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 853.0 ave 853.0 max 853.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 330.0 ave 330.0 max 330.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 660.0 ave 660.0 max 660.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 660
Ave neighs/atom = 330.0
Neighbor list builds = 0
Dangerous builds = 0
uncompute snap
unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 0
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
SNAP keyword elems A
SNAP keyword radelems 2.3
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector
thermo_style custom 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]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:694)
thermo_modify norm no
run ${nsteps}
run 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 1 1 1
5 neighbor lists, perpetual/occasional/extra = 1 4 0
(1) pair zbl, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute snav/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute snad/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(5) compute mliap, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 22.89 | 22.89 | 22.89 Mbytes
PotEng 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]
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
100.0% CPU use with 1 MPI tasks x no 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 | | 1e-06 | | |100.00
Nlocal: 2.0 ave 2.0 max 2.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 853.0 ave 853.0 max 853.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 330.0 ave 330.0 max 330.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 660.0 ave 660.0 max 660.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 660
Ave neighs/atom = 330.0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00