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update examples for removal of reax and meam

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This commit is contained in:
Axel Kohlmeyer
2018-12-10 15:16:34 -05:00
parent 1933c2eb5f
commit 0b5c273e2d
12 changed files with 2 additions and 1171 deletions
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examples/meam/in.meam
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# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
#dump 1 all atom 50 dump.meam
#dump 2 all image 10 image.*.jpg element element &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Si C
#dump 3 all movie 10 movie.mpg element element &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Si C
run 100

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examples/meam/log.27Nov18.meam.g++.1
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 1 by 1 MPI processor grid
reading atoms ...
128 atoms
pair_style meam
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
pair_coeff * * library.meam Si C SiC.meam Si C
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file SiC.meam with DATE: 2007-06-11
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
#dump 1 all atom 50 dump.meam
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Si C
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Si C
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.38121 0 -636.38121 -76571.819
10 1807.8862 -666.21959 0 -636.54126 -150571.49
20 1932.4467 -668.2581 0 -636.53498 -120223.52
30 1951.3652 -668.58139 0 -636.54771 -100508.4
40 2172.5974 -672.22715 0 -636.5617 -110753.34
50 2056.9149 -670.33108 0 -636.56468 -105418.07
60 1947.9564 -668.52788 0 -636.55015 -111413.04
70 1994.7712 -669.28849 0 -636.54225 -109645.76
80 2126.0903 -671.43755 0 -636.53557 -97475.831
90 2065.755 -670.4349 0 -636.52338 -95858.837
100 2051.4553 -670.20799 0 -636.53122 -107068.9
Loop time of 0.0545483 on 1 procs for 100 steps with 128 atoms
Performance: 158.392 ns/day, 0.152 hours/ns, 1833.239 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.050821 | 0.050821 | 0.050821 | 0.0 | 93.17
Neigh | 0.0026484 | 0.0026484 | 0.0026484 | 0.0 | 4.86
Comm | 0.0006423 | 0.0006423 | 0.0006423 | 0.0 | 1.18
Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.21
Modify | 0.00021195 | 0.00021195 | 0.00021195 | 0.0 | 0.39
Other | | 0.0001101 | | | 0.20
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 543 ave 543 max 543 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1526 ave 1526 max 1526 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3052 ave 3052 max 3052 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3052
Ave neighs/atom = 23.8438
Neighbor list builds = 10
Dangerous builds = 10
Total wall time: 0:00:00

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examples/meam/log.27Nov18.meam.g++.4
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 2 by 2 MPI processor grid
reading atoms ...
128 atoms
pair_style meam
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
pair_coeff * * library.meam Si C SiC.meam Si C
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file SiC.meam with DATE: 2007-06-11
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
#dump 1 all atom 50 dump.meam
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Si C
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Si C
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.38121 0 -636.38121 -76571.819
10 1807.8862 -666.21959 0 -636.54126 -150571.49
20 1932.4467 -668.2581 0 -636.53498 -120223.52
30 1951.3652 -668.58139 0 -636.54771 -100508.4
40 2172.5974 -672.22715 0 -636.5617 -110753.34
50 2056.9149 -670.33108 0 -636.56468 -105418.07
60 1947.9564 -668.52788 0 -636.55015 -111413.04
70 1994.7712 -669.28849 0 -636.54225 -109645.76
80 2126.0903 -671.43755 0 -636.53557 -97475.831
90 2065.755 -670.4349 0 -636.52338 -95858.837
100 2051.4553 -670.20799 0 -636.53122 -107068.9
Loop time of 0.023721 on 4 procs for 100 steps with 128 atoms
Performance: 364.234 ns/day, 0.066 hours/ns, 4215.667 timesteps/s
95.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.019888 | 0.020242 | 0.020626 | 0.2 | 85.33
Neigh | 0.00071859 | 0.00076133 | 0.00082922 | 0.0 | 3.21
Comm | 0.0019681 | 0.0022618 | 0.002651 | 0.5 | 9.53
Output | 0.00018048 | 0.0002225 | 0.00034213 | 0.0 | 0.94
Modify | 8.2016e-05 | 8.6308e-05 | 9.203e-05 | 0.0 | 0.36
Other | | 0.000147 | | | 0.62
Nlocal: 32 ave 36 max 30 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 293.75 ave 305 max 285 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 381.5 ave 413 max 334 min
Histogram: 1 0 0 0 1 0 0 0 0 2
FullNghs: 763 ave 866 max 678 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 3052
Ave neighs/atom = 23.8438
Neighbor list builds = 10
Dangerous builds = 10
Total wall time: 0:00:00

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examples/meam/log.27Nov18.meam.shear.g++.1
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
Time spent = 0.0007267 secs
pair_style meam
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam with DATE: 2007-06-11
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
timestep 0.001
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 27 17 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02
50 300 -8149.7654 0 -8096.1353 10633.141 19684.382
75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745
100 300 -8173.6884 0 -8120.0584 5952.521 19886.589
Loop time of 0.894544 on 1 procs for 100 steps with 1912 atoms
Performance: 9.659 ns/day, 2.485 hours/ns, 111.789 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.87012 | 0.87012 | 0.87012 | 0.0 | 97.27
Neigh | 0.01798 | 0.01798 | 0.01798 | 0.0 | 2.01
Comm | 0.0016143 | 0.0016143 | 0.0016143 | 0.0 | 0.18
Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.01
Modify | 0.0035381 | 0.0035381 | 0.0035381 | 0.0 | 0.40
Other | | 0.001176 | | | 0.13
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1672 ave 1672 max 1672 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23806 ave 23806 max 23806 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 47612 ave 47612 max 47612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 47612
Ave neighs/atom = 24.9017
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
#dump 1 all atom 500 dump.meam.shear
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
reset_timestep 0
run 3000
Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300.39988 -8173.6884 0 -8137.8874 4992.9811 19894.297
100 292.06374 -8177.7096 0 -8142.9021 2568.3762 19871.53
200 306.69894 -8177.1357 0 -8140.584 874.24259 20047.24
300 295.68229 -8172.9213 0 -8137.6825 -1049.0836 20091.759
400 308.99958 -8169.6355 0 -8132.8096 -1785.9335 20121.698
500 303.85723 -8163.984 0 -8127.7709 -150.56268 20183.813
600 300 -8157.7632 0 -8122.0099 1492.5742 20279.887
700 300 -8148.1328 0 -8112.3794 3506.9234 20435.302
800 300 -8139.1821 0 -8103.4288 3628.3957 20509.519
900 305.03425 -8126.7734 0 -8090.4201 5316.2206 20638.992
1000 304.00321 -8112.1616 0 -8075.9311 7441.9638 20767.243
1100 304.14041 -8096.5041 0 -8060.2573 9646.6972 20888.167
1200 302.78454 -8080.5931 0 -8044.5079 11516.208 20995.917
1300 308.67064 -8061.6724 0 -8024.8857 11496.471 21130.013
1400 309.82994 -8046.27 0 -8009.3451 12926.819 21247.271
1500 300 -8035.0317 0 -7999.2784 15346.797 21370.637
1600 300 -8030.6636 0 -7994.9102 14803.43 21496.446
1700 300 -8024.4819 0 -7988.7286 13175.257 21611.262
1800 300 -8022.8531 0 -7987.0998 10315.63 21743.178
1900 300 -8028.4095 0 -7992.6561 6882.0635 21855.551
2000 300 -8036.9005 0 -8001.1472 3508.9237 21983.802
2100 300 -8037.8224 0 -8002.0691 2724.0594 22112.054
2200 306.93248 -8035.3297 0 -7998.7501 4400.6008 22228.091
2300 306.24125 -8036.748 0 -8000.2508 6075.0546 22352.678
2400 300 -8038.8534 0 -8003.1 8701.8498 22465.051
2500 308.34129 -8034.0796 0 -7997.3322 10977.68 22600.632
2600 299.70072 -8028.8815 0 -7993.1638 15468.97 22715.447
2700 298.78276 -8019.1655 0 -7983.5572 18076.132 22844.921
2800 305.57845 -8014.3542 0 -7977.936 17573.035 22962.179
2900 300 -8015.7677 0 -7980.0144 13461.463 23087.988
3000 300 -8010.5908 0 -7974.8375 9333.4855 23199.139
Loop time of 29.4592 on 1 procs for 3000 steps with 1912 atoms
Performance: 8.799 ns/day, 2.728 hours/ns, 101.836 timesteps/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 | 28.489 | 28.489 | 28.489 | 0.0 | 96.71
Neigh | 0.77356 | 0.77356 | 0.77356 | 0.0 | 2.63
Comm | 0.052517 | 0.052517 | 0.052517 | 0.0 | 0.18
Output | 0.00095224 | 0.00095224 | 0.00095224 | 0.0 | 0.00
Modify | 0.10813 | 0.10813 | 0.10813 | 0.0 | 0.37
Other | | 0.03525 | | | 0.12
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1668 ave 1668 max 1668 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23391 ave 23391 max 23391 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 46782 ave 46782 max 46782 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46782
Ave neighs/atom = 24.4676
Neighbor list builds = 219
Dangerous builds = 0
Total wall time: 0:00:30

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examples/meam/log.27Nov18.meam.shear.g++.4
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
Time spent = 0.000408649 secs
pair_style meam
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam with DATE: 2007-06-11
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
timestep 0.001
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 27 17 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02
50 300 -8150.0685 0 -8096.4384 10317.407 19685.743
75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814
100 300 -8176.5141 0 -8122.884 4162.2559 19873.327
Loop time of 0.263516 on 4 procs for 100 steps with 1912 atoms
Performance: 32.787 ns/day, 0.732 hours/ns, 379.483 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24401 | 0.2486 | 0.25128 | 0.6 | 94.34
Neigh | 0.0046518 | 0.0047416 | 0.0048261 | 0.1 | 1.80
Comm | 0.0054512 | 0.0082117 | 0.012793 | 3.1 | 3.12
Output | 0.00010562 | 0.00013095 | 0.00019932 | 0.0 | 0.05
Modify | 0.0010016 | 0.0010275 | 0.0010595 | 0.1 | 0.39
Other | | 0.0008045 | | | 0.31
Nlocal: 478 ave 492 max 465 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 809 ave 822 max 795 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 5916 ave 6133 max 5658 min
Histogram: 1 0 0 1 0 0 0 0 1 1
FullNghs: 11832 ave 12277 max 11299 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 47328
Ave neighs/atom = 24.7531
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
#dump 1 all atom 500 dump.meam.shear
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
reset_timestep 0
run 3000
Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 295.32113 -8176.5141 0 -8141.3183 3169.3113 19886.93
100 292.00251 -8176.5358 0 -8141.7356 -825.04802 19918.765
200 306.11682 -8176.7719 0 -8140.2895 -1370.6886 19948.877
300 300 -8172.6262 0 -8136.8729 -1735.9765 20085.714
400 306.88489 -8168.435 0 -8131.8611 -933.02058 20117.012
500 308.99003 -8166.2906 0 -8129.4658 -1049.3138 20198.256
600 304.23435 -8158.0946 0 -8121.8366 583.93595 20328.848
700 296.44479 -8149.7914 0 -8114.4618 1985.4155 20421.046
800 307.75738 -8139.1649 0 -8102.487 4319.078 20513.183
900 304.61422 -8126.9246 0 -8090.6214 6654.0962 20640.213
1000 300 -8113.8464 0 -8078.0931 7760.1237 20768.465
1100 300.17873 -8097.7469 0 -8061.9722 8438.1259 20874.731
1200 306.01441 -8083.3367 0 -8046.8665 10835.588 20994.432
1300 300 -8067.022 0 -8031.2687 11216.061 21126.348
1400 300 -8053.223 0 -8017.4696 10570.211 21253.378
1500 300 -8043.4848 0 -8007.7314 11360.762 21375.523
1600 300 -8034.6201 0 -7998.8667 11371.282 21498.889
1700 300 -8028.6797 0 -7992.9263 9596.8454 21613.705
1800 300 -8033.0802 0 -7997.3268 8767.8176 21743.178
1900 303.23288 -8035.1821 0 -7999.0434 8065.2879 21859.215
2000 300 -8025.0795 0 -7989.3262 9321.8098 21980.138
2100 300 -8041.3621 0 -8005.6088 6674.2623 22108.39
2200 300 -8039.7261 0 -8003.9727 7548.8847 22225.648
2300 300 -8052.3497 0 -8016.5964 8936.4935 22352.678
2400 300 -8049.395 0 -8013.6416 12633.909 22476.044
2500 308.48099 -8039.9448 0 -8003.1807 16242.081 22593.303
2600 300 -8032.1953 0 -7996.442 18386.669 22722.776
2700 303.49413 -8027.6563 0 -7991.4865 14415.581 22829.042
2800 304.13476 -8017.3394 0 -7981.0933 7457.1076 22953.629
2900 300 -8010.3658 0 -7974.6124 2815.5155 23074.552
3000 309.49253 -7999.74 0 -7962.8553 756.7511 23210.132
Loop time of 8.57528 on 4 procs for 3000 steps with 1912 atoms
Performance: 30.226 ns/day, 0.794 hours/ns, 349.843 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.0046 | 8.0451 | 8.1075 | 1.5 | 93.82
Neigh | 0.20142 | 0.20699 | 0.21469 | 1.2 | 2.41
Comm | 0.1972 | 0.2657 | 0.312 | 9.3 | 3.10
Output | 0.00087762 | 0.0015897 | 0.0037148 | 3.1 | 0.02
Modify | 0.030267 | 0.031624 | 0.032929 | 0.7 | 0.37
Other | | 0.02427 | | | 0.28
Nlocal: 478 ave 507 max 447 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 799.75 ave 842 max 763 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 5806.5 ave 6097 max 5507 min
Histogram: 1 0 1 0 0 0 0 1 0 1
FullNghs: 11613 ave 12159 max 11039 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 46452
Ave neighs/atom = 24.295
Neighbor list builds = 224
Dangerous builds = 0
Total wall time: 0:00:08

8
examples/reax/README
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@ -1,12 +1,8 @@
This directory contains input files for two short ReaxFF simulations This directory contains input files for two short ReaxFF simulations
(RDX and TATB crystals) using the ReaxFF parameterization developed (RDX and TATB crystals) using the ReaxFF parameterization developed
for nitramines. The parameter file ffield.reax is the same as that in for nitramines. The parameter file ffield.reax is the same as that in
subdirectory RDX (see below). Input files for both pair_style reax and subdirectory RDX (see below). In addition, each subdirectory contains
pair_style reax/c are provided. validated parameter files for a particular published version of ReaxFF.
In addition, each subdirectory contains validated parameter files for
a particular published version of ReaxFF. In all cases, the examples
use pair_style reax/c.
Disclaimer: Using these force fields for systems they have not been Disclaimer: Using these force fields for systems they have not been
explicitly trained against may produce unrealistic results. Please explicitly trained against may produce unrealistic results. Please

52
examples/reax/in.reax.rdx
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# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
thermo 10
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb &
v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100

53
examples/reax/in.reax.tatb
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# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
thermo 5
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reax.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25

107
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair reax, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.278 | 3.278 | 3.278 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1885.1269 -1885.1269 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79973 0 168.8842
10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.02023 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.5115
20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134186 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574159
30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179958 0.049322453 0 78.853173 0.13604393 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.86177
40 647.45528 -1951.1994 -1912.6006 -5883.713 -2798.3556 17.334814 0.15102862 0 63.235117 0.18070924 -54.598957 0 17.325007 -12.052278 883.0167 -164.21335 0 96.777424
50 716.38088 -1949.4735 -1906.7656 5473.1969 -2800.9309 9.2056861 0.15413274 0 85.371466 3.2986127 -78.253597 0 34.861774 -8.553123 882.01431 -193.85254 0 117.21068
60 1175.2705 -1975.961 -1905.8958 -1939.4966 -2726.5816 -11.651996 0.24296786 0 48.320654 7.1799691 -75.363638 0 16.520127 -4.8869441 844.75401 -194.23297 0 119.73841
70 1156.701 -1975.3497 -1906.3916 24628.304 -2880.5225 25.652501 0.26894311 0 83.724852 7.1049152 -68.70096 0 24.750735 -8.6338267 911.20079 -183.40562 0 113.21047
80 840.23677 -1955.4769 -1905.3851 -17731.334 -2755.7299 -8.0167723 0.1386797 0 86.147417 2.2387319 -76.945843 0 23.595869 -7.260968 853.63487 -167.88288 0 94.603961
90 365.79122 -1926.4061 -1904.599 898.38479 -2842.1832 47.368107 0.23109002 0 92.288071 0.38031213 -61.361485 0 18.476336 -12.25546 900.24233 -186.48046 0 116.88827
100 801.32158 -1953.418 -1905.6462 -2417.6887 -2802.7247 4.6676477 0.18046575 0 76.729987 5.4177322 -77.102566 0 24.997175 -7.7554074 898.67337 -196.89114 0 120.38946
Loop time of 0.463306 on 1 procs for 100 steps with 21 atoms
Performance: 18.649 ns/day, 1.287 hours/ns, 215.840 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.46143 | 0.46143 | 0.46143 | 0.0 | 99.60
Neigh | 0.00087953 | 0.00087953 | 0.00087953 | 0.0 | 0.19
Comm | 0.00042653 | 0.00042653 | 0.00042653 | 0.0 | 0.09
Output | 0.00034237 | 0.00034237 | 0.00034237 | 0.0 | 0.07
Modify | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.02
Other | | 0.000124 | | | 0.03
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1106 ave 1106 max 1106 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1106
Ave neighs/atom = 52.6667
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

107
examples/reax/log.8March18.reax.rdx.g++.4
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair reax, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.262 | 3.36 | 3.647 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.88428
10 1281.7558 -1989.1322 -1912.7187 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.51152
20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134187 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574168
30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179959 0.049322449 0 78.853173 0.13604392 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.861765
40 647.45479 -1951.1995 -1912.6007 -5883.7199 -2798.3556 17.334805 0.15102868 0 63.235116 0.18070946 -54.59897 0 17.32501 -12.052277 883.0166 -164.21339 0 96.777473
50 716.37927 -1949.466 -1906.7582 5473.2486 -2800.9309 9.2056758 0.15413278 0 85.37143 3.2986099 -78.253596 0 34.861773 -8.5531243 882.01424 -193.85223 0 117.21791
60 1175.2698 -1975.9612 -1905.896 -1939.5206 -2726.5818 -11.651942 0.24296793 0 48.320679 7.1799538 -75.36365 0 16.520134 -4.8869515 844.75405 -194.23289 0 119.7383
70 1156.6963 -1975.3494 -1906.3915 24628.423 -2880.5221 25.65242 0.26894312 0 83.724787 7.1049615 -68.700925 0 24.750729 -8.6338123 911.2006 -183.40591 0 113.21091
80 840.238 -1955.4788 -1905.387 -17731.371 -2755.7301 -8.0167357 0.13868007 0 86.147246 2.2387405 -76.945868 0 23.595868 -7.2609697 853.6349 -167.88312 0 94.602512
90 365.78645 -1926.4072 -1904.6004 898.36945 -2842.1831 47.368307 0.23108998 0 92.288039 0.38031101 -61.361464 0 18.476388 -12.255481 900.24216 -186.48066 0 116.88716
100 801.31322 -1953.4165 -1905.6452 -2417.2041 -2802.7247 4.6678077 0.18046498 0 76.730367 5.4176812 -77.102592 0 24.9973 -7.7554425 898.6732 -196.89097 0 120.39043
Loop time of 0.404551 on 4 procs for 100 steps with 21 atoms
Performance: 21.357 ns/day, 1.124 hours/ns, 247.188 timesteps/s
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.2191 | 0.28038 | 0.39839 | 13.2 | 69.31
Neigh | 5.8651e-05 | 0.00025928 | 0.00062203 | 0.0 | 0.06
Comm | 0.0046599 | 0.12307 | 0.1845 | 19.9 | 30.42
Output | 0.00055337 | 0.00062728 | 0.00071192 | 0.0 | 0.16
Modify | 5.3167e-05 | 7.844e-05 | 0.00010109 | 0.0 | 0.02
Other | | 0.0001363 | | | 0.03
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 301.25 ave 827 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1205
Ave neighs/atom = 57.381
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

103
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reax.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair reax, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.764 | 7.764 | 7.764 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
5 0.63682806 -44767.737 -44767.01 8391.5964 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2728 0 6388.8127
10 2.4306958 -44769.409 -44766.634 11717.376 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0693 0 6381.7942
15 5.0590493 -44772.631 -44766.855 17125.067 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28962 -1566.5961 252.97781 -654.93836 18835.335 -8719.3013 0 6370.4551
20 8.067859 -44775.936 -44766.725 24620.627 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3748 0 6355.1614
25 10.975538 -44777.233 -44764.702 34381.173 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.23109 -1582.8552 253.88696 -653.46042 18790.855 -8683.8691 0 6336.3409
Loop time of 7.80129 on 1 procs for 25 steps with 384 atoms
Performance: 0.017 ns/day, 1386.896 hours/ns, 3.205 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.7384 | 7.7384 | 7.7384 | 0.0 | 99.19
Neigh | 0.058615 | 0.058615 | 0.058615 | 0.0 | 0.75
Comm | 0.0022428 | 0.0022428 | 0.0022428 | 0.0 | 0.03
Output | 0.00033212 | 0.00033212 | 0.00033212 | 0.0 | 0.00
Modify | 0.0013618 | 0.0013618 | 0.0013618 | 0.0 | 0.02
Other | | 0.0003309 | | | 0.00
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286828
Ave neighs/atom = 746.948
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:08

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examples/reax/log.8March18.reax.tatb.g++.4
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reax.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair reax, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
5 0.63682727 -44767.816 -44767.089 8391.1708 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3973 0 6388.8581
10 2.4306941 -44769.405 -44766.63 11717.306 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.08 0 6381.8083
15 5.0590444 -44772.6 -44766.824 17125.207 -61103.34 489.28008 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.2653 0 6370.4505
20 8.0678523 -44775.983 -44766.772 24620.114 -61088.791 490.42348 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.5228 0 6355.2629
25 10.975532 -44777.234 -44764.704 34381.065 -61068.889 490.53151 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.898 0 6336.3682
Loop time of 3.74388 on 4 procs for 25 steps with 384 atoms
Performance: 0.036 ns/day, 665.579 hours/ns, 6.678 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.478 | 3.6025 | 3.7215 | 4.8 | 96.22
Neigh | 0.012731 | 0.01299 | 0.013174 | 0.2 | 0.35
Comm | 0.0073411 | 0.12653 | 0.25119 | 25.4 | 3.38
Output | 0.00050354 | 0.00081849 | 0.0011628 | 0.0 | 0.02
Modify | 0.00049281 | 0.00082356 | 0.001157 | 0.0 | 0.02
Other | | 0.0002663 | | | 0.01
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 319016
Ave neighs/atom = 830.771
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:03