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Merge pull request #3795 from jwillma2/develop

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Adding carbon SNAP potential files and example
This commit is contained in:
Axel Kohlmeyer
2023-05-30 15:10:58 -04:00
committed by GitHub
parent ed03d04a70 da7a348089
commit 2a799d45a9
7 changed files with 1855 additions and 0 deletions
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examples/snap/C_SNAP_2021.10.15.quadratic.snapcoeff Symbolic link
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../../potentials/C_SNAP_2021.10.15.quadratic.snapcoeff

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examples/snap/C_SNAP_2021.10.15.quadratic.snapparam Symbolic link
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../../potentials/C_SNAP_2021.10.15.quadratic.snapparam

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examples/snap/in.C_SNAP Normal file
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#Carbon SNAP example: 216 atom diamond unit cell simulated NVT at ~1,000GPa and 5,000K
units metal
atom_style atomic
boundary p p p
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Crystal orientation and MD box creation #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
lattice diamond 2.845
region Bbox block 0 3 0 3 0 3
create_box 1 Bbox
create_atoms 1 region Bbox basis 1 1
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Interatomic potential parameters #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Specify hybrid with SNAP, ZBL, and long-range C_SNAP_2021.10.15.quadratic.ulomb
pair_style hybrid/overlay zbl 0.1 0.2 snap
pair_coeff 1 1 zbl 10 10
pair_coeff * * snap C_SNAP_2021.10.15.quadratic.snapcoeff C_SNAP_2021.10.15.quadratic.snapparam C
mass * 12.01
velocity all create 8000.0 3412461 loop geom
fix NVE all nve
fix NVT all langevin 5000.0 5000.0 0.1 3216548
thermo 50
thermo_style custom step temp ke pe etotal press pxx pyy pzz
run 500

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examples/snap/log.30May23.C_SNAP.g++.1 Normal file
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LAMMPS (28 Mar 2023 - Development)
using 1 OpenMP thread(s) per MPI task
#Carbon SNAP example: 216 atom diamond unit cell simulated NVT at ~1,000GPa and 5,000K
units metal
atom_style atomic
boundary p p p
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Crystal orientation and MD box creation #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
lattice diamond 2.845
Lattice spacing in x,y,z = 2.845 2.845 2.845
region Bbox block 0 3 0 3 0 3
create_box 1 Bbox
Created orthogonal box = (0 0 0) to (8.535 8.535 8.535)
1 by 1 by 1 MPI processor grid
create_atoms 1 region Bbox basis 1 1
Created 216 atoms
using lattice units in orthogonal box = (0 0 0) to (8.535 8.535 8.535)
create_atoms CPU = 0.000 seconds
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Interatomic potential parameters #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Specify hybrid with SNAP, ZBL, and long-range C_SNAP_2021.10.15.quadratic.ulomb
pair_style hybrid/overlay zbl 0.1 0.2 snap
pair_coeff 1 1 zbl 10 10
pair_coeff * * snap C_SNAP_2021.10.15.quadratic.snapcoeff C_SNAP_2021.10.15.quadratic.snapparam C
SNAP Element = C, Radius 0.5, Weight 1
SNAP keyword rcutfac 2.7
SNAP keyword twojmax 8
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0.0
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 1
mass * 12.01
velocity all create 8000.0 3412461 loop geom
fix NVE all nve
fix NVT all langevin 5000.0 5000.0 0.1 3216548
thermo 50
thermo_style custom step temp ke pe etotal press pxx pyy pzz
run 500
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.7
ghost atom cutoff = 4.7
binsize = 2.35, bins = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair zbl, perpetual, half/full trim from (2)
attributes: half, newton on, cut 2.2
pair build: halffull/newton/trim
stencil: none
bin: none
(2) pair snap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.835 | 4.835 | 4.835 Mbytes
Step Temp KinEng PotEng TotEng Press Pxx Pyy Pzz
0 8000 222.32745 -846.66062 -624.33318 10234249 10210805 10267435 10224506
50 4199.4229 116.70587 -723.2423 -606.53643 10256033 10157803 10280166 10330129
100 3820.2509 106.16833 -710.43537 -604.26704 10232872 10216484 10241309 10240825
150 4413.2948 122.64957 -710.09702 -587.44745 10254093 10323013 10265454 10173810
200 4688.024 130.28455 -702.26198 -571.97742 10306186 10281632 10342390 10294536
250 4997.165 138.87587 -720.58476 -581.70889 10284438 10220856 10360231 10272226
300 4640.4911 128.96357 -710.75063 -581.78706 10263301 10264007 10290526 10235369
350 4929.5117 136.99572 -707.2526 -570.25688 10290742 10359920 10284236 10228071
400 4700.9354 130.64337 -697.90277 -567.2594 10250682 10277287 10246032 10228729
450 5108.4971 141.96989 -700.57144 -558.60155 10289765 10323648 10306588 10239058
500 5146.7039 143.03169 -700.33221 -557.30052 10334303 10349736 10358785 10294387
Loop time of 36.7771 on 1 procs for 500 steps with 216 atoms
Performance: 1.175 ns/day, 20.432 hours/ns, 13.595 timesteps/s, 2.937 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 36.766 | 36.766 | 36.766 | 0.0 | 99.97
Neigh | 0.0010226 | 0.0010226 | 0.0010226 | 0.0 | 0.00
Comm | 0.0033205 | 0.0033205 | 0.0033205 | 0.0 | 0.01
Output | 0.00020657 | 0.00020657 | 0.00020657 | 0.0 | 0.00
Modify | 0.0047621 | 0.0047621 | 0.0047621 | 0.0 | 0.01
Other | | 0.001464 | | | 0.00
Nlocal: 216 ave 216 max 216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1746 ave 1746 max 1746 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1767 ave 1767 max 1767 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 32846 ave 32846 max 32846 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 32846
Ave neighs/atom = 152.06481
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:36

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examples/snap/log.30May23.C_SNAP.g++.4 Normal file
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LAMMPS (28 Mar 2023 - Development)
using 1 OpenMP thread(s) per MPI task
#Carbon SNAP example: 216 atom diamond unit cell simulated NVT at ~1,000GPa and 5,000K
units metal
atom_style atomic
boundary p p p
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Crystal orientation and MD box creation #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
lattice diamond 2.845
Lattice spacing in x,y,z = 2.845 2.845 2.845
region Bbox block 0 3 0 3 0 3
create_box 1 Bbox
Created orthogonal box = (0 0 0) to (8.535 8.535 8.535)
1 by 2 by 2 MPI processor grid
create_atoms 1 region Bbox basis 1 1
Created 216 atoms
using lattice units in orthogonal box = (0 0 0) to (8.535 8.535 8.535)
create_atoms CPU = 0.000 seconds
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Interatomic potential parameters #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Specify hybrid with SNAP, ZBL, and long-range C_SNAP_2021.10.15.quadratic.ulomb
pair_style hybrid/overlay zbl 0.1 0.2 snap
pair_coeff 1 1 zbl 10 10
pair_coeff * * snap C_SNAP_2021.10.15.quadratic.snapcoeff C_SNAP_2021.10.15.quadratic.snapparam C
SNAP Element = C, Radius 0.5, Weight 1
SNAP keyword rcutfac 2.7
SNAP keyword twojmax 8
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0.0
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 1
mass * 12.01
velocity all create 8000.0 3412461 loop geom
fix NVE all nve
fix NVT all langevin 5000.0 5000.0 0.1 3216548
thermo 50
thermo_style custom step temp ke pe etotal press pxx pyy pzz
run 500
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.7
ghost atom cutoff = 4.7
binsize = 2.35, bins = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair zbl, perpetual, half/full trim from (2)
attributes: half, newton on, cut 2.2
pair build: halffull/newton/trim
stencil: none
bin: none
(2) pair snap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.681 | 4.681 Mbytes
Step Temp KinEng PotEng TotEng Press Pxx Pyy Pzz
0 8000 222.32745 -846.66062 -624.33318 10234249 10210805 10267435 10224506
50 4382.3571 121.78978 -715.70492 -593.91513 10262157 10278549 10181545 10326376
100 4546.1549 126.34188 -713.11818 -586.77631 10261694 10257647 10333666 10193770
150 5109.4576 141.99658 -708.87952 -566.88294 10268132 10248182 10248240 10307974
200 4764.2181 132.40206 -712.16881 -579.76675 10329903 10238991 10379394 10371323
250 4989.5099 138.66313 -710.39748 -571.73435 10282678 10321057 10274124 10252854
300 4853.3102 134.87801 -699.98167 -565.10366 10343314 10204138 10430172 10395634
350 4788.1153 133.06618 -705.14381 -572.07763 10325571 10312657 10267999 10396058
400 5055.7813 140.50487 -707.38537 -566.8805 10323176 10357258 10310733 10301536
450 5182.3198 144.02149 -695.11614 -551.09465 10345564 10358486 10346325 10331881
500 5311.077 147.59977 -691.32767 -543.7279 10308823 10242668 10214102 10469700
Loop time of 11.5932 on 4 procs for 500 steps with 216 atoms
Performance: 3.726 ns/day, 6.441 hours/ns, 43.129 timesteps/s, 9.316 katom-step/s
94.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.241 | 10.446 | 10.695 | 5.0 | 90.11
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.87613 | 1.1187 | 1.3179 | 14.9 | 9.65
Output | 0.0002656 | 0.0010016 | 0.0015521 | 1.5 | 0.01
Modify | 0.0019493 | 0.0020668 | 0.0021577 | 0.2 | 0.02
Other | | 0.02508 | | | 0.22
Nlocal: 54 ave 54 max 54 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1082 ave 1082 max 1082 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 432 ave 432 max 432 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 8532 ave 8532 max 8532 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 34128
Ave neighs/atom = 158
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:11

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potentials/C_SNAP_2021.10.15.quadratic.snapcoeff Normal file
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potentials/C_SNAP_2021.10.15.quadratic.snapparam Normal file
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# required
rcutfac 2.7
twojmax 8
# optional
rfac0 0.99363
rmin0 0.0
bzeroflag 0
quadraticflag 1