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simplify and shorten example, use symlinks, recreate logs

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This commit is contained in:
Axel Kohlmeyer
2023-05-30 14:24:32 -04:00
parent 2855f18d02
commit da7a348089
7 changed files with 226 additions and 1778 deletions
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1602
examples/snap/C_SNAP_2021.10.15.quadratic.snapcoeff
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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
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# required
rcutfac 2.7
twojmax 8
# optional
rfac0 0.99363
rmin0 0.0
bzeroflag 0
quadraticflag 1

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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
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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
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# User-defined variables #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
variable alat equal "2.845"
variable nx equal "3"
variable ny equal "3"
variable nz equal "3"
variable tstep equal "0.000500"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Crystal orientation and MD box creation #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
lattice diamond ${alat}
region Bbox block 0 ${nx} 0 ${ny} 0 ${nz}
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 #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
include pot_C.mod
# 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. 5000. 0.1 3216548
thermo 100
thermo_style custom step temp ke pe etotal pxx pyy pzz xlo xhi ylo yhi zlo zhi cpu
run 2000
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.23May23.C_SNAP
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LAMMPS (3 Aug 2022)
units metal
atom_style atomic
boundary p p p
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# User-defined variables #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
variable alat equal "2.845"
variable nx equal "3"
variable ny equal "3"
variable nz equal "3"
variable tstep equal "0.000500"
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Crystal orientation and MD box creation #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
lattice diamond ${alat}
lattice diamond 2.845
Lattice spacing in x,y,z = 2.845 2.845 2.845
region Bbox block 0 ${nx} 0 ${ny} 0 ${nz}
region Bbox block 0 3 0 ${ny} 0 ${nz}
region Bbox block 0 3 0 3 0 ${nz}
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 #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
include pot_C.mod
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 0.1 #0.38
variable zblcutouter equal 0.2
variable zblz equal 10 #500
# Specify hybrid with SNAP, ZBL, and long-range C_SNAP_2021.10.15.quadratic.ulomb
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 0.1 ${zblcutouter} snap
pair_style hybrid/overlay zbl 0.1 0.2 snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 10 ${zblz}
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
fix NVE all nve
fix NVT all langevin 5000. 5000. 0.1 3216548
thermo 100
thermo_style custom step temp ke pe etotal pxx pyy pzz xlo xhi ylo yhi zlo zhi cpu
run 2000
Neighbor list info ...
update: every = 1 steps, delay = 10 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 Pxx Pyy Pzz Xlo Xhi Ylo Yhi Zlo Zhi CPU
0 0 0 -846.66062 -846.66062 9852302.8 9852302.8 9852302.8 0 8.535 0 8.535 0 8.535 0
100 2994.9404 83.232183 -760.46784 -677.23566 10153319 10162613 10089556 0 8.535 0 8.535 0 8.535 8.5637966
200 4138.1573 115.00324 -718.21196 -603.20871 10328838 10278023 10147395 0 8.535 0 8.535 0 8.535 17.231147
300 4231.1241 117.58688 -703.12914 -585.54226 10229126 10278574 10244536 0 8.535 0 8.535 0 8.535 25.883724
400 4902.5771 136.24718 -693.59525 -557.34807 10258619 10309837 10270759 0 8.535 0 8.535 0 8.535 34.454573
500 5231.01 145.37464 -703.59176 -558.21712 10380296 10313494 10261486 0 8.535 0 8.535 0 8.535 43.03519
600 4962.4828 137.91202 -701.69725 -563.78524 10405175 10240153 10223683 0 8.535 0 8.535 0 8.535 51.617418
700 5158.8211 143.36844 -696.3068 -552.93836 10224265 10353872 10237323 0 8.535 0 8.535 0 8.535 60.216592
800 5566.4588 154.69707 -691.80266 -537.10558 10345764 10333822 10328272 0 8.535 0 8.535 0 8.535 68.836406
900 4763.5973 132.38481 -699.56143 -567.17663 10265807 10264115 10292086 0 8.535 0 8.535 0 8.535 77.557491
1000 5374.1522 149.35269 -707.77182 -558.41912 10353688 10245807 10289801 0 8.535 0 8.535 0 8.535 86.134981
1100 4729.9838 131.45065 -687.84753 -556.39687 10236271 10295262 10280036 0 8.535 0 8.535 0 8.535 94.80143
1200 5524.4648 153.53002 -688.33164 -534.80162 10376941 10311014 10272151 0 8.535 0 8.535 0 8.535 103.66054
1300 5424.1134 150.74116 -710.48851 -559.74735 10269935 10381675 10208553 0 8.535 0 8.535 0 8.535 112.29193
1400 5082.4497 141.24601 -703.51889 -562.27288 10289096 10270701 10360960 0 8.535 0 8.535 0 8.535 120.98393
1500 4782.7699 132.91763 -709.97393 -577.0563 10264631 10200017 10341446 0 8.535 0 8.535 0 8.535 129.56238
1600 5080.7401 141.1985 -693.90867 -552.71017 10263936 10300165 10411302 0 8.535 0 8.535 0 8.535 138.13256
1700 5192.8466 144.31404 -698.99608 -554.68204 10309414 10291531 10256424 0 8.535 0 8.535 0 8.535 146.75162
1800 5105.1385 141.87655 -702.43759 -560.56104 10325438 10245469 10330602 0 8.535 0 8.535 0 8.535 155.63637
1900 5015.6808 139.39044 -706.73213 -567.34169 10345833 10310789 10319358 0 8.535 0 8.535 0 8.535 164.26556
2000 4894.0288 136.00962 -697.34077 -561.33115 10259839 10328896 10230941 0 8.535 0 8.535 0 8.535 172.92786
Loop time of 172.928 on 1 procs for 2000 steps with 216 atoms
Performance: 0.999 ns/day, 24.018 hours/ns, 11.566 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 172.88 | 172.88 | 172.88 | 0.0 | 99.97
Neigh | 0.0050877 | 0.0050877 | 0.0050877 | 0.0 | 0.00
Comm | 0.013326 | 0.013326 | 0.013326 | 0.0 | 0.01
Output | 0.001194 | 0.001194 | 0.001194 | 0.0 | 0.00
Modify | 0.022687 | 0.022687 | 0.022687 | 0.0 | 0.01
Other | | 0.006874 | | | 0.00
Nlocal: 216 ave 216 max 216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1806 ave 1806 max 1806 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1782 ave 1782 max 1782 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 32872 ave 32872 max 32872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 32872
Ave neighs/atom = 152.18519
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:02:53

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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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examples/snap/pot_C.mod
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# Definition of SNAP+ZBL potential.
variable zblcutinner equal 0.1
variable zblcutouter equal 0.2
variable zblz equal 10
# Specify hybrid with SNAP, ZBL, and long-range C_SNAP_2021.10.15.quadratic.ulomb
pair_style hybrid/overlay &
zbl ${zblcutinner} ${zblcutouter} &
snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff * * snap C_SNAP_2021.10.15.quadratic.snapcoeff C_SNAP_2021.10.15.quadratic.snapparam C