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provide new reference outputs for various reaxff examples

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This commit is contained in:
Axel Kohlmeyer
2018-03-08 18:10:28 -05:00
parent 0c4c002f34
commit fcfbdb13ab
34 changed files with 1405 additions and 859 deletions
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70
examples/reax/AB/log.5Oct16.AB.g++.4
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LAMMPS (5 Oct 2016)
# REAX potential for Nitroamines system
# .....
units real
atom_style charge
read_data data.AB
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
104 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.AB H B N
Reading potential file ffield.reax.AB with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.ab
run 3000
Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5
Memory usage per processor = 12.622 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
3000 496.56561 -8405.3755 0 -8252.9182 472.58916
Loop time of 7.23109 on 4 procs for 3000 steps with 104 atoms
Performance: 8.961 ns/day, 2.678 hours/ns, 414.875 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.705 | 5.7262 | 5.7504 | 0.7 | 79.19
Neigh | 0.14367 | 0.15976 | 0.16805 | 2.4 | 2.21
Comm | 0.053353 | 0.077311 | 0.097821 | 5.7 | 1.07
Output | 1.812e-05 | 1.9848e-05 | 2.408e-05 | 0.1 | 0.00
Modify | 1.2559 | 1.2647 | 1.2818 | 0.9 | 17.49
Other | | 0.003126 | | | 0.04
Nlocal: 26 ave 35 max 13 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 421 ave 450 max 377 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 847.25 ave 1149 max 444 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 3389
Ave neighs/atom = 32.5865
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:07

47
examples/reax/AB/log.5Oct16.AB.g++.1 → examples/reax/AB/log.8Mar18.AB.g++.1
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LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system # REAX potential for Nitroamines system
# ..... # .....
@ -28,43 +29,53 @@ timestep 0.25
run 3000 run 3000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5
Memory usage per processor = 18.4119 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 19.3 | 19.3 | 19.3 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566 0 0 -8505.1816 0 -8505.1816 -673.36566
3000 499.30579 -8405.1387 0 -8251.8401 -94.844317 3000 478.18595 -8398.4168 0 -8251.6025 1452.6935
Loop time of 12.5114 on 1 procs for 3000 steps with 104 atoms Loop time of 14.3573 on 1 procs for 3000 steps with 104 atoms
Performance: 5.179 ns/day, 4.634 hours/ns, 239.782 timesteps/s Performance: 4.513 ns/day, 5.318 hours/ns, 208.952 timesteps/s
99.3% CPU use with 1 MPI tasks x no OpenMP threads 96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 11.137 | 11.137 | 11.137 | 0.0 | 89.01 Pair | 12.709 | 12.709 | 12.709 | 0.0 | 88.52
Neigh | 0.29816 | 0.29816 | 0.29816 | 0.0 | 2.38 Neigh | 0.36804 | 0.36804 | 0.36804 | 0.0 | 2.56
Comm | 0.016993 | 0.016993 | 0.016993 | 0.0 | 0.14 Comm | 0.022419 | 0.022419 | 0.022419 | 0.0 | 0.16
Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00 Output | 2.8133e-05 | 2.8133e-05 | 2.8133e-05 | 0.0 | 0.00
Modify | 1.0552 | 1.0552 | 1.0552 | 0.0 | 8.43 Modify | 1.2513 | 1.2513 | 1.2513 | 0.0 | 8.72
Other | | 0.004142 | | | 0.03 Other | | 0.006263 | | | 0.04
Nlocal: 104 ave 104 max 104 min Nlocal: 104 ave 104 max 104 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 694 ave 694 max 694 min Nghost: 694 ave 694 max 694 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2927 ave 2927 max 2927 min Neighs: 2866 ave 2866 max 2866 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2927 Total # of neighbors = 2866
Ave neighs/atom = 28.1442 Ave neighs/atom = 27.5577
Neighbor list builds = 300 Neighbor list builds = 300
Dangerous builds not checked Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:12 Total wall time: 0:00:14

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examples/reax/AB/log.8Mar18.AB.g++.4 Normal file
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
units real
atom_style charge
read_data data.AB
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
104 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.AB H B N
Reading potential file ffield.reax.AB with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.ab
run 3000
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 12.38 | 13.22 | 13.64 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
3000 555.17702 -8426.5541 0 -8256.1017 219.26856
Loop time of 9.03521 on 4 procs for 3000 steps with 104 atoms
Performance: 7.172 ns/day, 3.346 hours/ns, 332.034 timesteps/s
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.0347 | 7.0652 | 7.1049 | 1.0 | 78.20
Neigh | 0.18481 | 0.20727 | 0.22108 | 3.0 | 2.29
Comm | 0.075175 | 0.11496 | 0.14517 | 7.4 | 1.27
Output | 2.2888e-05 | 2.569e-05 | 3.1948e-05 | 0.0 | 0.00
Modify | 1.6286 | 1.6421 | 1.6649 | 1.1 | 18.17
Other | | 0.005646 | | | 0.06
Nlocal: 26 ave 35 max 13 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 420.25 ave 454 max 370 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 862.5 ave 1178 max 444 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 3450
Ave neighs/atom = 33.1731
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09

41
examples/reax/AuO/log.5Oct16.AuO.g++.1 → examples/reax/AuO/log.8Mar18.AuO.g++.1
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for AuO system # REAX potential for AuO system
# ..... # .....
@ -28,30 +29,40 @@ timestep 0.25
run 100 run 100
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 4 5 binsize = 6, bins = 5 4 5
Memory usage per processor = 144.382 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 157.6 | 157.6 | 157.6 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -72201.743 0 -72201.743 -166.1947 0 0 -72201.743 0 -72201.743 -166.19482
100 69.043346 -72076.31 0 -71878.943 22702.308 100 69.043331 -72076.309 0 -71878.942 22702.89
Loop time of 17.7559 on 1 procs for 100 steps with 960 atoms Loop time of 18.4369 on 1 procs for 100 steps with 960 atoms
Performance: 0.122 ns/day, 197.288 hours/ns, 5.632 timesteps/s Performance: 0.117 ns/day, 204.854 hours/ns, 5.424 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 15.102 | 15.102 | 15.102 | 0.0 | 85.05 Pair | 15.373 | 15.373 | 15.373 | 0.0 | 83.38
Neigh | 0.49358 | 0.49358 | 0.49358 | 0.0 | 2.78 Neigh | 0.58774 | 0.58774 | 0.58774 | 0.0 | 3.19
Comm | 0.0067561 | 0.0067561 | 0.0067561 | 0.0 | 0.04 Comm | 0.0079026 | 0.0079026 | 0.0079026 | 0.0 | 0.04
Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Output | 3.171e-05 | 3.171e-05 | 3.171e-05 | 0.0 | 0.00
Modify | 2.1525 | 2.1525 | 2.1525 | 0.0 | 12.12 Modify | 2.4665 | 2.4665 | 2.4665 | 0.0 | 13.38
Other | | 0.001267 | | | 0.01 Other | | 0.001366 | | | 0.01
Nlocal: 960 ave 960 max 960 min Nlocal: 960 ave 960 max 960 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

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examples/reax/AuO/log.5Oct16.AuO.g++.4 → examples/reax/AuO/log.8Mar18.AuO.g++.4
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LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for AuO system # REAX potential for AuO system
# ..... # .....
@ -28,30 +29,40 @@ timestep 0.25
run 100 run 100
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 4 5 binsize = 6, bins = 5 4 5
Memory usage per processor = 80.1039 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 87.17 | 87.17 | 87.17 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -72201.743 0 -72201.743 -166.20356 0 0 -72201.743 0 -72201.743 -166.2027
100 69.043372 -72076.31 0 -71878.943 22701.855 100 69.043379 -72076.31 0 -71878.943 22701.771
Loop time of 7.66838 on 4 procs for 100 steps with 960 atoms Loop time of 8.44797 on 4 procs for 100 steps with 960 atoms
Performance: 0.282 ns/day, 85.204 hours/ns, 13.041 timesteps/s Performance: 0.256 ns/day, 93.866 hours/ns, 11.837 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads 96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 6.7833 | 6.7864 | 6.7951 | 0.2 | 88.50 Pair | 7.3702 | 7.3757 | 7.3879 | 0.3 | 87.31
Neigh | 0.2412 | 0.24206 | 0.24396 | 0.2 | 3.16 Neigh | 0.28875 | 0.29449 | 0.29747 | 0.6 | 3.49
Comm | 0.010402 | 0.019419 | 0.022561 | 3.7 | 0.25 Comm | 0.015008 | 0.027055 | 0.032681 | 4.3 | 0.32
Output | 2.0981e-05 | 2.3007e-05 | 2.9087e-05 | 0.1 | 0.00 Output | 2.4319e-05 | 2.8551e-05 | 3.8624e-05 | 0.0 | 0.00
Modify | 0.61733 | 0.61964 | 0.62064 | 0.2 | 8.08 Modify | 0.74721 | 0.74985 | 0.75539 | 0.4 | 8.88
Other | | 0.0007888 | | | 0.01 Other | | 0.0008975 | | | 0.01
Nlocal: 240 ave 240 max 240 min Nlocal: 240 ave 240 max 240 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
@ -67,4 +78,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:07 Total wall time: 0:00:08

43
examples/reax/CHO/log.5Oct16.CHO.g++.1 → examples/reax/CHO/log.8Mar18.CHO.g++.1
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LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for CHO system # REAX potential for CHO system
# ..... # .....
@ -28,30 +29,40 @@ timestep 0.25
run 3000 run 3000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5
Memory usage per processor = 17.7936 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -10226.557 0 -10226.557 -106.09789 0 0 -10226.557 0 -10226.557 -106.09755
3000 548.72503 -10170.457 0 -10000.349 34.314945 3000 548.5116 -10170.389 0 -10000.348 40.372297
Loop time of 11.5678 on 1 procs for 3000 steps with 105 atoms Loop time of 12.6046 on 1 procs for 3000 steps with 105 atoms
Performance: 5.602 ns/day, 4.284 hours/ns, 259.340 timesteps/s Performance: 5.141 ns/day, 4.668 hours/ns, 238.008 timesteps/s
99.3% CPU use with 1 MPI tasks x no OpenMP threads 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 10.111 | 10.111 | 10.111 | 0.0 | 87.41 Pair | 10.931 | 10.931 | 10.931 | 0.0 | 86.72
Neigh | 0.27992 | 0.27992 | 0.27992 | 0.0 | 2.42 Neigh | 0.33107 | 0.33107 | 0.33107 | 0.0 | 2.63
Comm | 0.01603 | 0.01603 | 0.01603 | 0.0 | 0.14 Comm | 0.017975 | 0.017975 | 0.017975 | 0.0 | 0.14
Output | 1.2159e-05 | 1.2159e-05 | 1.2159e-05 | 0.0 | 0.00 Output | 2.0742e-05 | 2.0742e-05 | 2.0742e-05 | 0.0 | 0.00
Modify | 1.1563 | 1.1563 | 1.1563 | 0.0 | 10.00 Modify | 1.3197 | 1.3197 | 1.3197 | 0.0 | 10.47
Other | | 0.004084 | | | 0.04 Other | | 0.005059 | | | 0.04
Nlocal: 105 ave 105 max 105 min Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -67,4 +78,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:11 Total wall time: 0:00:12

43
examples/reax/CHO/log.5Oct16.CHO.g++.4 → examples/reax/CHO/log.8Mar18.CHO.g++.4
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for CHO system # REAX potential for CHO system
# ..... # .....
@ -28,30 +29,40 @@ timestep 0.25
run 3000 run 3000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5
Memory usage per processor = 12.9938 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 11.75 | 12.85 | 13.81 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -10226.557 0 -10226.557 -106.0974 0 0 -10226.557 0 -10226.557 -106.09745
3000 547.91377 -10170.194 0 -10000.338 61.118402 3000 548.30567 -10170.323 0 -10000.346 47.794514
Loop time of 6.51546 on 4 procs for 3000 steps with 105 atoms Loop time of 7.42367 on 4 procs for 3000 steps with 105 atoms
Performance: 9.946 ns/day, 2.413 hours/ns, 460.443 timesteps/s Performance: 8.729 ns/day, 2.750 hours/ns, 404.113 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads 97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 4.9869 | 5.0615 | 5.1246 | 2.3 | 77.68 Pair | 5.3058 | 5.4086 | 5.4922 | 3.1 | 72.86
Neigh | 0.12213 | 0.14723 | 0.17304 | 5.5 | 2.26 Neigh | 0.14791 | 0.17866 | 0.2106 | 6.5 | 2.41
Comm | 0.05189 | 0.11582 | 0.18932 | 15.4 | 1.78 Comm | 0.080185 | 0.16666 | 0.26933 | 17.7 | 2.24
Output | 1.812e-05 | 2.0564e-05 | 2.5988e-05 | 0.1 | 0.00 Output | 2.5988e-05 | 2.8491e-05 | 3.4571e-05 | 0.0 | 0.00
Modify | 1.1626 | 1.1878 | 1.2122 | 1.9 | 18.23 Modify | 1.6364 | 1.6658 | 1.6941 | 2.0 | 22.44
Other | | 0.003059 | | | 0.05 Other | | 0.003964 | | | 0.05
Nlocal: 26.25 ave 45 max 6 min Nlocal: 26.25 ave 45 max 6 min
Histogram: 1 0 1 0 0 0 0 0 1 1 Histogram: 1 0 1 0 0 0 0 0 1 1
@ -67,4 +78,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:06 Total wall time: 0:00:07

59
examples/reax/FC/log.5Oct16.FC.g++.1 → examples/reax/FC/log.8Mar18.FC.g++.1
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system # REAX potential for Nitroamines system
# ..... # .....
@ -29,13 +30,23 @@ thermo 1
dump 4 all xyz 5000 dumpnpt.xyz dump 4 all xyz 5000 dumpnpt.xyz
run 10 run 10
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 28 27 17 binsize = 6, bins = 28 27 17
Memory usage per processor = 440.212 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes
Step Temp E_pair TotEng Press Step Temp E_pair TotEng Press
0 0 -808525.04 -808525.04 58194.694 0 0 -808525.04 -808525.04 58194.694
1 4.9935726 -808803.89 -808546.69 58205.825 1 4.9935726 -808803.89 -808546.69 58205.825
@ -48,20 +59,20 @@ Step Temp E_pair TotEng Press
8 320.17692 -826387.27 -809896.43 58886.877 8 320.17692 -826387.27 -809896.43 58886.877
9 404.17073 -831129.48 -810312.5 59064.551 9 404.17073 -831129.48 -810312.5 59064.551
10 497.02486 -836425.19 -810825.72 59260.714 10 497.02486 -836425.19 -810825.72 59260.714
Loop time of 20.3094 on 1 procs for 10 steps with 17280 atoms Loop time of 21.5054 on 1 procs for 10 steps with 17280 atoms
Performance: 0.009 ns/day, 2820.746 hours/ns, 0.492 timesteps/s Performance: 0.008 ns/day, 2986.857 hours/ns, 0.465 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 18.124 | 18.124 | 18.124 | 0.0 | 89.24 Pair | 19.008 | 19.008 | 19.008 | 0.0 | 88.39
Neigh | 0.072459 | 0.072459 | 0.072459 | 0.0 | 0.36 Neigh | 0.084401 | 0.084401 | 0.084401 | 0.0 | 0.39
Comm | 0.00077629 | 0.00077629 | 0.00077629 | 0.0 | 0.00 Comm | 0.00080419 | 0.00080419 | 0.00080419 | 0.0 | 0.00
Output | 0.00075412 | 0.00075412 | 0.00075412 | 0.0 | 0.00 Output | 0.00095367 | 0.00095367 | 0.00095367 | 0.0 | 0.00
Modify | 2.1109 | 2.1109 | 2.1109 | 0.0 | 10.39 Modify | 2.4109 | 2.4109 | 2.4109 | 0.0 | 11.21
Other | | 0.0005426 | | | 0.00 Other | | 0.0004592 | | | 0.00
Nlocal: 17280 ave 17280 max 17280 min Nlocal: 17280 ave 17280 max 17280 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -85,7 +96,7 @@ timestep 0.2
#dump 6 all custom 5000 dumpidtype.dat id type x y z #dump 6 all custom 5000 dumpidtype.dat id type x y z
run 10 run 10
Memory usage per processor = 440.212 Mbytes Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes
Step Temp E_pair TotEng Press Step Temp E_pair TotEng Press
10 497.02486 -836425.19 -810825.72 59260.714 10 497.02486 -836425.19 -810825.72 59260.714
11 601.65141 -841814.22 -810825.91 59489.422 11 601.65141 -841814.22 -810825.91 59489.422
@ -98,20 +109,20 @@ Step Temp E_pair TotEng Press
18 1623.072 -894534.04 -810937.04 61739.541 18 1623.072 -894534.04 -810937.04 61739.541
19 1812.1865 -904337.99 -811000.57 62200.561 19 1812.1865 -904337.99 -811000.57 62200.561
20 2011.5899 -915379.19 -811771.41 63361.151 20 2011.5899 -915379.19 -811771.41 63361.151
Loop time of 20.3051 on 1 procs for 10 steps with 17280 atoms Loop time of 21.362 on 1 procs for 10 steps with 17280 atoms
Performance: 0.009 ns/day, 2820.155 hours/ns, 0.492 timesteps/s Performance: 0.008 ns/day, 2966.945 hours/ns, 0.468 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 18.008 | 18.008 | 18.008 | 0.0 | 88.69 Pair | 18.793 | 18.793 | 18.793 | 0.0 | 87.97
Neigh | 0.069963 | 0.069963 | 0.069963 | 0.0 | 0.34 Neigh | 0.077047 | 0.077047 | 0.077047 | 0.0 | 0.36
Comm | 0.00077033 | 0.00077033 | 0.00077033 | 0.0 | 0.00 Comm | 0.00080276 | 0.00080276 | 0.00080276 | 0.0 | 0.00
Output | 0.00077224 | 0.00077224 | 0.00077224 | 0.0 | 0.00 Output | 0.0010097 | 0.0010097 | 0.0010097 | 0.0 | 0.00
Modify | 2.225 | 2.225 | 2.225 | 0.0 | 10.96 Modify | 2.4897 | 2.4897 | 2.4897 | 0.0 | 11.65
Other | | 0.0005276 | | | 0.00 Other | | 0.0004568 | | | 0.00
Nlocal: 17280 ave 17280 max 17280 min Nlocal: 17280 ave 17280 max 17280 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -127,4 +138,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:45 Total wall time: 0:00:47

59
examples/reax/FC/log.5Oct16.FC.g++.4 → examples/reax/FC/log.8Mar18.FC.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system # REAX potential for Nitroamines system
# ..... # .....
@ -29,13 +30,23 @@ thermo 1
dump 4 all xyz 5000 dumpnpt.xyz dump 4 all xyz 5000 dumpnpt.xyz
run 10 run 10
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 28 27 17 binsize = 6, bins = 28 27 17
Memory usage per processor = 140.018 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes
Step Temp E_pair TotEng Press Step Temp E_pair TotEng Press
0 0 -808525.04 -808525.04 58194.694 0 0 -808525.04 -808525.04 58194.694
1 4.9935726 -808803.89 -808546.69 58205.825 1 4.9935726 -808803.89 -808546.69 58205.825
@ -48,20 +59,20 @@ Step Temp E_pair TotEng Press
8 320.17692 -826387.27 -809896.43 58886.877 8 320.17692 -826387.27 -809896.43 58886.877
9 404.17073 -831129.48 -810312.5 59064.551 9 404.17073 -831129.48 -810312.5 59064.551
10 497.02486 -836425.19 -810825.72 59260.714 10 497.02486 -836425.19 -810825.72 59260.714
Loop time of 5.47494 on 4 procs for 10 steps with 17280 atoms Loop time of 6.02109 on 4 procs for 10 steps with 17280 atoms
Performance: 0.032 ns/day, 760.408 hours/ns, 1.827 timesteps/s Performance: 0.029 ns/day, 836.262 hours/ns, 1.661 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads 99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 4.5958 | 4.7748 | 4.8852 | 5.4 | 87.21 Pair | 4.9482 | 5.1186 | 5.3113 | 7.4 | 85.01
Neigh | 0.021961 | 0.022104 | 0.022431 | 0.1 | 0.40 Neigh | 0.024811 | 0.025702 | 0.027556 | 0.7 | 0.43
Comm | 0.0077388 | 0.11804 | 0.29694 | 34.2 | 2.16 Comm | 0.0027421 | 0.19541 | 0.36565 | 38.1 | 3.25
Output | 0.00047708 | 0.00051123 | 0.0005939 | 0.2 | 0.01 Output | 0.00053239 | 0.00057119 | 0.00067186 | 0.0 | 0.01
Modify | 0.55906 | 0.55927 | 0.55946 | 0.0 | 10.22 Modify | 0.67876 | 0.68059 | 0.68165 | 0.1 | 11.30
Other | | 0.0002034 | | | 0.00 Other | | 0.0001779 | | | 0.00
Nlocal: 4320 ave 4320 max 4320 min Nlocal: 4320 ave 4320 max 4320 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
@ -85,7 +96,7 @@ timestep 0.2
#dump 6 all custom 5000 dumpidtype.dat id type x y z #dump 6 all custom 5000 dumpidtype.dat id type x y z
run 10 run 10
Memory usage per processor = 140.018 Mbytes Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes
Step Temp E_pair TotEng Press Step Temp E_pair TotEng Press
10 497.02486 -836425.19 -810825.72 59260.714 10 497.02486 -836425.19 -810825.72 59260.714
11 601.65141 -841814.22 -810825.91 59489.422 11 601.65141 -841814.22 -810825.91 59489.422
@ -98,20 +109,20 @@ Step Temp E_pair TotEng Press
18 1623.072 -894534.04 -810937.04 61739.541 18 1623.072 -894534.04 -810937.04 61739.541
19 1812.1865 -904337.99 -811000.57 62200.561 19 1812.1865 -904337.99 -811000.57 62200.561
20 2011.5899 -915379.19 -811771.41 63361.151 20 2011.5899 -915379.19 -811771.41 63361.151
Loop time of 5.49026 on 4 procs for 10 steps with 17280 atoms Loop time of 6.08805 on 4 procs for 10 steps with 17280 atoms
Performance: 0.031 ns/day, 762.536 hours/ns, 1.821 timesteps/s Performance: 0.028 ns/day, 845.563 hours/ns, 1.643 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads 99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 4.5657 | 4.7603 | 4.8596 | 5.4 | 86.70 Pair | 4.9124 | 5.1008 | 5.3405 | 8.3 | 83.78
Neigh | 0.021023 | 0.021468 | 0.022176 | 0.3 | 0.39 Neigh | 0.023652 | 0.024473 | 0.025996 | 0.6 | 0.40
Comm | 0.016467 | 0.1157 | 0.31031 | 34.7 | 2.11 Comm | 0.0020971 | 0.24171 | 0.43023 | 38.0 | 3.97
Output | 0.00047684 | 0.00050694 | 0.00059295 | 0.2 | 0.01 Output | 0.00056076 | 0.00060701 | 0.00072312 | 0.0 | 0.01
Modify | 0.59135 | 0.59207 | 0.59251 | 0.1 | 10.78 Modify | 0.71869 | 0.72023 | 0.72107 | 0.1 | 11.83
Other | | 0.0001938 | | | 0.00 Other | | 0.0001827 | | | 0.00
Nlocal: 4320 ave 4320 max 4320 min Nlocal: 4320 ave 4320 max 4320 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
@ -127,4 +138,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:12 Total wall time: 0:00:13

8
examples/reax/HNS/in.reaxc.hns
View File

@ -1,6 +1,12 @@
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS # Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
# See README for more info # See README for more info
variable x index 2
variable y index 2
variable z index 2
variable t index 100
units real units real
atom_style charge atom_style charge
atom_modify sort 100 0.0 # optional atom_modify sort 100 0.0 # optional
@ -24,7 +30,7 @@ timestep 0.1
thermo_style custom step temp pe press evdwl ecoul vol thermo_style custom step temp pe press evdwl ecoul vol
thermo_modify norm yes thermo_modify norm yes
thermo 100 thermo 10
velocity all create 300.0 41279 loop geom velocity all create 300.0 41279 loop geom

115
examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1 Normal file
View File

@ -0,0 +1,115 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
# See README for more info
variable x index 2
variable y index 2
variable z index 2
variable t index 100
units real
atom_style charge
atom_modify sort 100 0.0 # optional
dimension 3
boundary p p p
box tilt large
read_data data.hns-equil
triclinic box = (0 0 0) to (22.326 11.1412 13.779) with tilt (0 -5.02603 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
304 atoms
reading velocities ...
304 velocities
replicate $x $y $z bbox
replicate 2 $y $z bbox
replicate 2 2 $z bbox
replicate 2 2 2 bbox
triclinic box = (0 0 0) to (44.652 22.2824 27.5579) with tilt (0 -10.0521 0)
1 by 1 by 1 MPI processor grid
2432 atoms
Time spent = 0.000789404 secs
pair_style reax/c NULL
pair_coeff * * ffield.reax.hns C H O N
compute reax all pair reax/c
neighbor 1.0 bin
neigh_modify every 20 delay 0 check no
timestep 0.1
thermo_style custom step temp pe press evdwl ecoul vol
thermo_modify norm yes
thermo 10
velocity all create 300.0 41279 loop geom
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
run 100
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 10 5 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 262.4 | 262.4 | 262.4 Mbytes
Step Temp PotEng Press E_vdwl E_coul Volume
0 300 -113.27833 437.52103 -111.57687 -1.7014647 27418.867
10 299.87174 -113.27778 2033.6337 -111.57645 -1.7013325 27418.867
20 300.81718 -113.28046 4817.5889 -111.57931 -1.7011463 27418.867
30 301.8622 -113.28323 8303.0039 -111.58237 -1.7008608 27418.867
40 302.4646 -113.28493 10519.459 -111.58446 -1.700467 27418.867
50 300.79064 -113.27989 10402.291 -111.57987 -1.7000218 27418.867
60 296.11534 -113.26599 7929.1348 -111.5664 -1.6995929 27418.867
70 291.73354 -113.25289 5071.5459 -111.5537 -1.6991916 27418.867
80 292.189 -113.25399 5667.0962 -111.55519 -1.6987993 27418.867
90 298.40792 -113.27253 7513.3806 -111.57409 -1.6984403 27418.867
100 303.58246 -113.28809 10017.879 -111.58991 -1.698177 27418.867
Loop time of 59.5461 on 1 procs for 100 steps with 2432 atoms
Performance: 0.015 ns/day, 1654.060 hours/ns, 1.679 timesteps/s
97.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 49.922 | 49.922 | 49.922 | 0.0 | 83.84
Neigh | 0.53154 | 0.53154 | 0.53154 | 0.0 | 0.89
Comm | 0.011399 | 0.011399 | 0.011399 | 0.0 | 0.02
Output | 0.00064397 | 0.00064397 | 0.00064397 | 0.0 | 0.00
Modify | 9.0782 | 9.0782 | 9.0782 | 0.0 | 15.25
Other | | 0.002116 | | | 0.00
Nlocal: 2432 ave 2432 max 2432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10687 ave 10687 max 10687 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 823977 ave 823977 max 823977 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 823977
Ave neighs/atom = 338.806
Neighbor list builds = 5
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:00

115
examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4 Normal file
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@ -0,0 +1,115 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
# See README for more info
variable x index 2
variable y index 2
variable z index 2
variable t index 100
units real
atom_style charge
atom_modify sort 100 0.0 # optional
dimension 3
boundary p p p
box tilt large
read_data data.hns-equil
triclinic box = (0 0 0) to (22.326 11.1412 13.779) with tilt (0 -5.02603 0)
2 by 1 by 2 MPI processor grid
reading atoms ...
304 atoms
reading velocities ...
304 velocities
replicate $x $y $z bbox
replicate 2 $y $z bbox
replicate 2 2 $z bbox
replicate 2 2 2 bbox
triclinic box = (0 0 0) to (44.652 22.2824 27.5579) with tilt (0 -10.0521 0)
2 by 1 by 2 MPI processor grid
2432 atoms
Time spent = 0.000398397 secs
pair_style reax/c NULL
pair_coeff * * ffield.reax.hns C H O N
compute reax all pair reax/c
neighbor 1.0 bin
neigh_modify every 20 delay 0 check no
timestep 0.1
thermo_style custom step temp pe press evdwl ecoul vol
thermo_modify norm yes
thermo 10
velocity all create 300.0 41279 loop geom
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
run 100
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 10 5 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 126.6 | 126.6 | 126.6 Mbytes
Step Temp PotEng Press E_vdwl E_coul Volume
0 300 -113.27833 437.52112 -111.57687 -1.7014647 27418.867
10 299.87174 -113.27778 2033.632 -111.57645 -1.7013325 27418.867
20 300.81719 -113.28046 4817.5761 -111.57931 -1.7011463 27418.867
30 301.8622 -113.28323 8302.9767 -111.58237 -1.7008609 27418.867
40 302.4646 -113.28493 10519.481 -111.58446 -1.700467 27418.867
50 300.79064 -113.27989 10402.312 -111.57987 -1.7000217 27418.867
60 296.11534 -113.26599 7929.1393 -111.5664 -1.6995929 27418.867
70 291.73354 -113.25289 5071.5368 -111.5537 -1.6991916 27418.867
80 292.18901 -113.25399 5667.1118 -111.55519 -1.6987993 27418.867
90 298.40793 -113.27253 7513.4029 -111.57409 -1.6984403 27418.867
100 303.58247 -113.28809 10017.892 -111.58991 -1.698177 27418.867
Loop time of 21.3933 on 4 procs for 100 steps with 2432 atoms
Performance: 0.040 ns/day, 594.257 hours/ns, 4.674 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.863 | 16.367 | 18.027 | 28.6 | 76.51
Neigh | 0.23943 | 0.2422 | 0.24658 | 0.6 | 1.13
Comm | 0.024331 | 1.6845 | 3.189 | 89.2 | 7.87
Output | 0.00051165 | 0.00056899 | 0.00068665 | 0.0 | 0.00
Modify | 3.0933 | 3.0969 | 3.0999 | 0.1 | 14.48
Other | | 0.001784 | | | 0.01
Nlocal: 608 ave 608 max 608 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5738.25 ave 5742 max 5734 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 231544 ave 231625 max 231466 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 926176
Ave neighs/atom = 380.829
Neighbor list builds = 5
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:21

47
examples/reax/RDX/log.5Oct16.RDX.g++.1 → examples/reax/RDX/log.8Mar18.RDX.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems # REAX potential for high energy CHON systems
# ..... # .....
@ -28,43 +29,53 @@ timestep 0.25
run 3000 run 3000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5
Memory usage per processor = 18.1116 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 19 | 19 | 19 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -10197.932 0 -10197.932 38.347492 0 0 -10197.932 0 -10197.932 38.347492
3000 510.85923 -10091.694 0 -9933.3253 1668.5084 3000 510.63767 -10091.537 0 -9933.2374 1144.545
Loop time of 18.9088 on 1 procs for 3000 steps with 105 atoms Loop time of 21.2931 on 1 procs for 3000 steps with 105 atoms
Performance: 3.427 ns/day, 7.003 hours/ns, 158.657 timesteps/s Performance: 3.043 ns/day, 7.886 hours/ns, 140.891 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads 97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 17.724 | 17.724 | 17.724 | 0.0 | 93.73 Pair | 19.887 | 19.887 | 19.887 | 0.0 | 93.40
Neigh | 0.27457 | 0.27457 | 0.27457 | 0.0 | 1.45 Neigh | 0.33143 | 0.33143 | 0.33143 | 0.0 | 1.56
Comm | 0.015814 | 0.015814 | 0.015814 | 0.0 | 0.08 Comm | 0.02079 | 0.02079 | 0.02079 | 0.0 | 0.10
Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00 Output | 2.5272e-05 | 2.5272e-05 | 2.5272e-05 | 0.0 | 0.00
Modify | 0.89014 | 0.89014 | 0.89014 | 0.0 | 4.71 Modify | 1.0478 | 1.0478 | 1.0478 | 0.0 | 4.92
Other | | 0.004246 | | | 0.02 Other | | 0.006125 | | | 0.03
Nlocal: 105 ave 105 max 105 min Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 645 ave 645 max 645 min Nghost: 645 ave 645 max 645 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3061 ave 3061 max 3061 min Neighs: 3063 ave 3063 max 3063 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3061 Total # of neighbors = 3063
Ave neighs/atom = 29.1524 Ave neighs/atom = 29.1714
Neighbor list builds = 300 Neighbor list builds = 300
Dangerous builds not checked Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:19 Total wall time: 0:00:21

47
examples/reax/RDX/log.5Oct16.RDX.g++.4 → examples/reax/RDX/log.8Mar18.RDX.g++.4
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems # REAX potential for high energy CHON systems
# ..... # .....
@ -28,43 +29,53 @@ timestep 0.25
run 3000 run 3000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5
Memory usage per processor = 12.2102 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 12.14 | 13.04 | 13.9 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -10197.932 0 -10197.932 38.347492 0 0 -10197.932 0 -10197.932 38.347492
3000 504.05354 -10089.494 0 -9933.2351 868.32505 3000 509.89257 -10091.36 0 -9933.2916 1406.1215
Loop time of 9.70759 on 4 procs for 3000 steps with 105 atoms Loop time of 10.8858 on 4 procs for 3000 steps with 105 atoms
Performance: 6.675 ns/day, 3.595 hours/ns, 309.037 timesteps/s Performance: 5.953 ns/day, 4.032 hours/ns, 275.588 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads 98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 8.4621 | 8.5307 | 8.6001 | 1.9 | 87.88 Pair | 9.3081 | 9.4054 | 9.4994 | 2.6 | 86.40
Neigh | 0.12583 | 0.14931 | 0.17341 | 4.5 | 1.54 Neigh | 0.15541 | 0.18258 | 0.2099 | 4.7 | 1.68
Comm | 0.053017 | 0.12311 | 0.19244 | 16.2 | 1.27 Comm | 0.070516 | 0.16621 | 0.26541 | 19.7 | 1.53
Output | 1.9073e-05 | 2.0802e-05 | 2.408e-05 | 0.0 | 0.00 Output | 2.2173e-05 | 2.5153e-05 | 3.3855e-05 | 0.0 | 0.00
Modify | 0.87638 | 0.9012 | 0.92557 | 1.9 | 9.28 Modify | 1.0979 | 1.1272 | 1.1568 | 2.1 | 10.35
Other | | 0.003213 | | | 0.03 Other | | 0.004379 | | | 0.04
Nlocal: 26.25 ave 46 max 8 min Nlocal: 26.25 ave 46 max 8 min
Histogram: 1 0 0 1 0 1 0 0 0 1 Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 399.5 ave 512 max 288 min Nghost: 399.5 ave 512 max 288 min
Histogram: 1 0 0 1 0 0 1 0 0 1 Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 1010.75 ave 1818 max 420 min Neighs: 1011.25 ave 1819 max 420 min
Histogram: 1 0 1 1 0 0 0 0 0 1 Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 4043 Total # of neighbors = 4045
Ave neighs/atom = 38.5048 Ave neighs/atom = 38.5238
Neighbor list builds = 300 Neighbor list builds = 300
Dangerous builds not checked Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:10 Total wall time: 0:00:11

70
examples/reax/VOH/log.5Oct16.VOH.g++.4
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@ -1,70 +0,0 @@
LAMMPS (5 Oct 2016)
# REAX potential for VOH system
# .....
units real
atom_style charge
read_data data.VOH
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
100 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.V_O_C_H H C O V
Reading potential file ffield.reax.V_O_C_H with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.voh
run 3000
Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5
Memory usage per processor = 12.1769 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10246.825 0 -10246.825 42.256092
3000 518.1493 -10196.234 0 -10043.328 -334.5971
Loop time of 5.59178 on 4 procs for 3000 steps with 100 atoms
Performance: 11.588 ns/day, 2.071 hours/ns, 536.502 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.2807 | 4.3532 | 4.398 | 2.1 | 77.85
Neigh | 0.12328 | 0.14561 | 0.16815 | 4.2 | 2.60
Comm | 0.051619 | 0.097282 | 0.1697 | 14.1 | 1.74
Output | 1.7881e-05 | 1.9372e-05 | 2.3842e-05 | 0.1 | 0.00
Modify | 0.9701 | 0.99258 | 1.0148 | 1.6 | 17.75
Other | | 0.003097 | | | 0.06
Nlocal: 25 ave 38 max 11 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 368.25 ave 449 max 283 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 1084.5 ave 1793 max 418 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 4338
Ave neighs/atom = 43.38
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:05

47
examples/reax/VOH/log.5Oct16.VOH.g++.1 → examples/reax/VOH/log.8Mar18.VOH.g++.1
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for VOH system # REAX potential for VOH system
# ..... # .....
@ -28,43 +29,53 @@ timestep 0.25
run 3000 run 3000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5
Memory usage per processor = 16.9211 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.79 | 17.79 | 17.79 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -10246.825 0 -10246.825 42.256089 0 0 -10246.825 0 -10246.825 42.256089
3000 479.39686 -10186.225 0 -10044.755 -454.82798 3000 476.73301 -10185.256 0 -10044.572 -694.70737
Loop time of 10.4348 on 1 procs for 3000 steps with 100 atoms Loop time of 11.0577 on 1 procs for 3000 steps with 100 atoms
Performance: 6.210 ns/day, 3.865 hours/ns, 287.499 timesteps/s Performance: 5.860 ns/day, 4.095 hours/ns, 271.304 timesteps/s
99.2% CPU use with 1 MPI tasks x no OpenMP threads 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 9.2216 | 9.2216 | 9.2216 | 0.0 | 88.37 Pair | 9.6785 | 9.6785 | 9.6785 | 0.0 | 87.53
Neigh | 0.2757 | 0.2757 | 0.2757 | 0.0 | 2.64 Neigh | 0.32599 | 0.32599 | 0.32599 | 0.0 | 2.95
Comm | 0.015626 | 0.015626 | 0.015626 | 0.0 | 0.15 Comm | 0.017231 | 0.017231 | 0.017231 | 0.0 | 0.16
Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00 Output | 2.5511e-05 | 2.5511e-05 | 2.5511e-05 | 0.0 | 0.00
Modify | 0.91782 | 0.91782 | 0.91782 | 0.0 | 8.80 Modify | 1.0311 | 1.0311 | 1.0311 | 0.0 | 9.32
Other | | 0.004039 | | | 0.04 Other | | 0.004857 | | | 0.04
Nlocal: 100 ave 100 max 100 min Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 598 ave 598 max 598 min Nghost: 598 ave 598 max 598 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3384 ave 3384 max 3384 min Neighs: 3390 ave 3390 max 3390 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3384 Total # of neighbors = 3390
Ave neighs/atom = 33.84 Ave neighs/atom = 33.9
Neighbor list builds = 300 Neighbor list builds = 300
Dangerous builds not checked Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:10 Total wall time: 0:00:11

81
examples/reax/VOH/log.8Mar18.VOH.g++.4 Normal file
View File

@ -0,0 +1,81 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for VOH system
# .....
units real
atom_style charge
read_data data.VOH
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
100 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.V_O_C_H H C O V
Reading potential file ffield.reax.V_O_C_H with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.voh
run 3000
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 11.21 | 12.52 | 13.64 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10246.825 0 -10246.825 42.256092
3000 489.67803 -10188.866 0 -10044.362 -553.7513
Loop time of 6.49847 on 4 procs for 3000 steps with 100 atoms
Performance: 9.972 ns/day, 2.407 hours/ns, 461.647 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.7412 | 4.8453 | 4.9104 | 2.9 | 74.56
Neigh | 0.1468 | 0.17834 | 0.20151 | 4.7 | 2.74
Comm | 0.071841 | 0.14037 | 0.24502 | 17.2 | 2.16
Output | 2.1219e-05 | 2.408e-05 | 3.1948e-05 | 0.0 | 0.00
Modify | 1.3072 | 1.3308 | 1.3627 | 1.7 | 20.48
Other | | 0.003713 | | | 0.06
Nlocal: 25 ave 38 max 11 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 369.75 ave 453 max 283 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 1082.25 ave 1788 max 417 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 4329
Ave neighs/atom = 43.29
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:06

47
examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.1 → examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for ZnOH2 system # REAX potential for ZnOH2 system
# ..... # .....
@ -28,43 +29,53 @@ timestep 0.25
run 3000 run 3000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5
Memory usage per processor = 17.485 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 18.36 | 18.36 | 18.36 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -7900.2668 0 -7900.2668 60.076093 0 0 -7900.2668 0 -7900.2668 60.076093
3000 522.42599 -7928.9641 0 -7767.0098 -755.28778 3000 535.58577 -7934.7287 0 -7768.6948 -475.46237
Loop time of 6.38119 on 1 procs for 3000 steps with 105 atoms Loop time of 7.29784 on 1 procs for 3000 steps with 105 atoms
Performance: 10.155 ns/day, 2.363 hours/ns, 470.132 timesteps/s Performance: 8.879 ns/day, 2.703 hours/ns, 411.081 timesteps/s
99.0% CPU use with 1 MPI tasks x no OpenMP threads 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 5.2711 | 5.2711 | 5.2711 | 0.0 | 82.60 Pair | 5.9988 | 5.9988 | 5.9988 | 0.0 | 82.20
Neigh | 0.30669 | 0.30669 | 0.30669 | 0.0 | 4.81 Neigh | 0.37455 | 0.37455 | 0.37455 | 0.0 | 5.13
Comm | 0.015599 | 0.015599 | 0.015599 | 0.0 | 0.24 Comm | 0.019186 | 0.019186 | 0.019186 | 0.0 | 0.26
Output | 1.0967e-05 | 1.0967e-05 | 1.0967e-05 | 0.0 | 0.00 Output | 2.4557e-05 | 2.4557e-05 | 2.4557e-05 | 0.0 | 0.00
Modify | 0.78376 | 0.78376 | 0.78376 | 0.0 | 12.28 Modify | 0.89915 | 0.89915 | 0.89915 | 0.0 | 12.32
Other | | 0.004036 | | | 0.06 Other | | 0.006108 | | | 0.08
Nlocal: 105 ave 105 max 105 min Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 649 ave 649 max 649 min Nghost: 649 ave 649 max 649 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3956 ave 3956 max 3956 min Neighs: 3971 ave 3971 max 3971 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3956 Total # of neighbors = 3971
Ave neighs/atom = 37.6762 Ave neighs/atom = 37.819
Neighbor list builds = 300 Neighbor list builds = 300
Dangerous builds not checked Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:06 Total wall time: 0:00:07

45
examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.4 → examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for ZnOH2 system # REAX potential for ZnOH2 system
# ..... # .....
@ -28,40 +29,50 @@ timestep 0.25
run 3000 run 3000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5
Memory usage per processor = 12.0066 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 11.28 | 12.77 | 14.21 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -7900.2668 0 -7900.2668 60.076093 0 0 -7900.2668 0 -7900.2668 60.076093
3000 536.8256 -7935.1437 0 -7768.7255 -479.27959 3000 538.25796 -7935.6159 0 -7768.7536 -525.47078
Loop time of 3.77632 on 4 procs for 3000 steps with 105 atoms Loop time of 4.48824 on 4 procs for 3000 steps with 105 atoms
Performance: 17.160 ns/day, 1.399 hours/ns, 794.423 timesteps/s Performance: 14.438 ns/day, 1.662 hours/ns, 668.414 timesteps/s
99.0% CPU use with 4 MPI tasks x no OpenMP threads 97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 2.7337 | 2.7808 | 2.8316 | 2.5 | 73.64 Pair | 3.1031 | 3.1698 | 3.2378 | 3.3 | 70.62
Neigh | 0.13455 | 0.16558 | 0.19493 | 5.3 | 4.38 Neigh | 0.16642 | 0.20502 | 0.25003 | 6.6 | 4.57
Comm | 0.046741 | 0.099375 | 0.14663 | 13.6 | 2.63 Comm | 0.074932 | 0.14224 | 0.21025 | 15.6 | 3.17
Output | 1.7881e-05 | 2.0027e-05 | 2.408e-05 | 0.1 | 0.00 Output | 0.00011349 | 0.00011736 | 0.00012231 | 0.0 | 0.00
Modify | 0.69792 | 0.7275 | 0.75887 | 2.5 | 19.26 Modify | 0.92089 | 0.96736 | 1.0083 | 3.2 | 21.55
Other | | 0.003084 | | | 0.08 Other | | 0.003731 | | | 0.08
Nlocal: 26.25 ave 45 max 15 min Nlocal: 26.25 ave 45 max 15 min
Histogram: 1 0 2 0 0 0 0 0 0 1 Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 399 ave 509 max 295 min Nghost: 399 ave 509 max 295 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 0 2 0 0 0 0 1
Neighs: 1150 ave 2061 max 701 min Neighs: 1151.5 ave 2066 max 701 min
Histogram: 1 2 0 0 0 0 0 0 0 1 Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 4600 Total # of neighbors = 4606
Ave neighs/atom = 43.8095 Ave neighs/atom = 43.8667
Neighbor list builds = 300 Neighbor list builds = 300
Dangerous builds not checked Dangerous builds not checked

0
examples/reax/ci-reaxFF/input.in → examples/reax/ci-reaxFF/in.ci-reax.CH
View File

24
examples/reax/ci-reaxFF/log.23Oct17.g++.1 → examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (23 Oct 2017) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
#ci-reax potential for CH systems with tabulated ZBL correction #ci-reax potential for CH systems with tabulated ZBL correction
atom_style charge atom_style charge
units real units real
@ -31,6 +32,7 @@ fix 2 all temp/berendsen 500.0 500.0 100.0
#dump 1 all atom 30 dump.ci-reax.lammpstrj #dump 1 all atom 30 dump.ci-reax.lammpstrj
run 3000 run 3000
WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (../pair_reaxc.cpp:392)
Neighbor list info ... Neighbor list info ...
update every 1 steps, delay 10 steps, check yes update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
@ -52,20 +54,20 @@ Per MPI rank memory allocation (min/avg/max) = 43.46 | 43.46 | 43.46 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 508.42043 -28736.654 0 -28260.785 1678.3276 0 508.42043 -28736.654 0 -28260.785 1678.3276
3000 480.41333 -28707.835 0 -28258.181 -3150.0762 3000 480.41333 -28707.835 0 -28258.181 -3150.0762
Loop time of 21.5509 on 1 procs for 3000 steps with 315 atoms Loop time of 45.3959 on 1 procs for 3000 steps with 315 atoms
Performance: 3.007 ns/day, 7.982 hours/ns, 139.205 timesteps/s Performance: 1.427 ns/day, 16.813 hours/ns, 66.085 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads 96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 21.315 | 21.315 | 21.315 | 0.0 | 98.91 Pair | 44.955 | 44.955 | 44.955 | 0.0 | 99.03
Neigh | 0.17846 | 0.17846 | 0.17846 | 0.0 | 0.83 Neigh | 0.29903 | 0.29903 | 0.29903 | 0.0 | 0.66
Comm | 0.028676 | 0.028676 | 0.028676 | 0.0 | 0.13 Comm | 0.056547 | 0.056547 | 0.056547 | 0.0 | 0.12
Output | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.00 Output | 4.8399e-05 | 4.8399e-05 | 4.8399e-05 | 0.0 | 0.00
Modify | 0.018969 | 0.018969 | 0.018969 | 0.0 | 0.09 Modify | 0.058722 | 0.058722 | 0.058722 | 0.0 | 0.13
Other | | 0.009438 | | | 0.04 Other | | 0.02632 | | | 0.06
Nlocal: 315 ave 315 max 315 min Nlocal: 315 ave 315 max 315 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -81,4 +83,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:21 Total wall time: 0:00:45

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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
#ci-reax potential for CH systems with tabulated ZBL correction
atom_style charge
units real
read_data CH4.dat
orthogonal box = (0 0 0) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
315 atoms
reading velocities ...
315 velocities
pair_style hybrid/overlay reax/c control checkqeq no table linear 11000
pair_coeff * * reax/c ffield.ci-reax.CH C H
Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
WARNING: 2 of 10000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
WARNING: 2 of 11000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
WARNING: 2 of 6000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
timestep 0.25
fix 1 all nve
fix 2 all temp/berendsen 500.0 500.0 100.0
#dump 1 all atom 30 dump.ci-reax.lammpstrj
run 3000
WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (../pair_reaxc.cpp:392)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9.5
ghost atom cutoff = 9.5
binsize = 4.75, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.48 | 25.61 | 27.27 Mbytes
Step Temp E_pair E_mol TotEng Press
0 508.42043 -28736.654 0 -28260.785 1678.3276
3000 480.41333 -28707.835 0 -28258.181 -3150.0762
Loop time of 24.7034 on 4 procs for 3000 steps with 315 atoms
Performance: 2.623 ns/day, 9.149 hours/ns, 121.441 timesteps/s
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.945 | 21.367 | 24.046 | 39.3 | 86.49
Neigh | 0.1456 | 0.15254 | 0.16101 | 1.6 | 0.62
Comm | 0.39168 | 3.0859 | 5.5185 | 103.9 | 12.49
Output | 3.5763e-05 | 4.065e-05 | 5.2452e-05 | 0.0 | 0.00
Modify | 0.05831 | 0.068811 | 0.077666 | 2.9 | 0.28
Other | | 0.0292 | | | 0.12
Nlocal: 78.75 ave 96 max 65 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1233 ave 1348 max 1116 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 9467.25 ave 12150 max 7160 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 37869
Ave neighs/atom = 120.219
Neighbor list builds = 37
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:24

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LAMMPS (5 Oct 2016)
# 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 will be deprecated soon - users should switch to pair_style reax/c (../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 ...
1 neighbor list requests
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
Memory usage per processor = 2.95105 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 -244.79971 0 168.88435
10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070522 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17724 0 107.5115
20 516.83079 -1941.677 -1910.8655 -12525.41 -2801.8626 7.4107974 0.073134188 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574158
30 467.2641 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179959 0.049322439 0 78.853175 0.13604392 -51.653634 0 19.862872 -9.7098575 853.79334 -151.232 0 80.861768
40 647.45541 -1951.1994 -1912.6006 -5883.7147 -2798.3556 17.334807 0.15102863 0 63.23512 0.18070931 -54.598962 0 17.325008 -12.052277 883.01667 -164.21335 0 96.777422
50 716.38057 -1949.4749 -1906.767 5473.2085 -2800.931 9.2056917 0.15413274 0 85.371449 3.2986106 -78.253597 0 34.861773 -8.5531236 882.01435 -193.85275 0 117.2096
60 1175.2707 -1975.9611 -1905.8959 -1939.4971 -2726.5816 -11.651982 0.24296788 0 48.320663 7.1799636 -75.363641 0 16.520132 -4.8869463 844.754 -194.23296 0 119.73837
70 1156.7 -1975.3486 -1906.3905 24628.344 -2880.5223 25.652478 0.26894312 0 83.724884 7.1049303 -68.700942 0 24.750744 -8.6338218 911.20067 -183.4058 0 113.21158
80 840.23687 -1955.4768 -1905.3851 -17731.383 -2755.7295 -8.0168306 0.13867962 0 86.14748 2.2387306 -76.945841 0 23.595858 -7.2609645 853.6346 -167.88289 0 94.603895
90 365.79169 -1926.406 -1904.5989 898.37155 -2842.183 47.368211 0.23109 0 92.288131 0.38031313 -61.361483 0 18.476377 -12.255472 900.24202 -186.48056 0 116.88831
100 801.32078 -1953.4177 -1905.646 -2417.5518 -2802.7244 4.6676973 0.18046558 0 76.730114 5.4177372 -77.102556 0 24.997234 -7.7554179 898.67306 -196.8912 0 120.38952
Loop time of 0.512828 on 1 procs for 100 steps with 21 atoms
Performance: 16.848 ns/day, 1.425 hours/ns, 194.997 timesteps/s
99.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.51126 | 0.51126 | 0.51126 | 0.0 | 99.69
Neigh | 0.00071597 | 0.00071597 | 0.00071597 | 0.0 | 0.14
Comm | 0.00040317 | 0.00040317 | 0.00040317 | 0.0 | 0.08
Output | 0.00027037 | 0.00027037 | 0.00027037 | 0.0 | 0.05
Modify | 7.2241e-05 | 7.2241e-05 | 7.2241e-05 | 0.0 | 0.01
Other | | 0.000108 | | | 0.02
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

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LAMMPS (5 Oct 2016)
# 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 will be deprecated soon - users should switch to pair_style reax/c (../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 ...
1 neighbor list requests
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
Memory usage per processor = 3.0718 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 0 168.8843
10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17725 0 107.51148
20 516.8308 -1941.677 -1910.8655 -12525.411 -2801.8626 7.4107973 0.07313419 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574155
30 467.26411 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179966 0.049322437 0 78.853175 0.13604391 -51.653634 0 19.862872 -9.7098574 853.79333 -151.232 0 80.861765
40 647.45584 -1951.1994 -1912.6006 -5883.7102 -2798.3557 17.334812 0.15102857 0 63.235124 0.18070914 -54.598951 0 17.325006 -12.052278 883.01674 -164.21335 0 96.777418
50 716.38108 -1949.4679 -1906.76 5473.1803 -2800.9311 9.2057064 0.15413272 0 85.371443 3.2986124 -78.253597 0 34.861778 -8.5531235 882.01441 -193.85213 0 117.21596
60 1175.2703 -1975.9632 -1905.898 -1939.6676 -2726.5815 -11.652032 0.24296779 0 48.320636 7.1799647 -75.363643 0 16.520124 -4.8869416 844.75396 -194.25563 0 119.75889
70 1156.7016 -1975.3469 -1906.3887 24628.125 -2880.5225 25.65252 0.26894309 0 83.724869 7.1048931 -68.700978 0 24.750754 -8.6338341 911.20067 -183.41947 0 113.22722
80 840.3323 -1955.4867 -1905.3893 -17732.956 -2755.7336 -8.0168615 0.13869303 0 86.143454 2.2388975 -76.946365 0 23.594977 -7.2608903 853.63682 -167.88599 0 94.604168
90 365.75853 -1926.4192 -1904.6141 902.29004 -2842.1715 47.360077 0.23110905 0 92.28805 0.38040356 -61.364192 0 18.473252 -12.253964 900.23128 -186.47889 0 116.88518
100 801.64661 -1953.4392 -1905.6481 -2464.5533 -2802.6922 4.6510183 0.18048786 0 76.715675 5.41849 -77.102069 0 24.987058 -7.7531389 898.65974 -196.87724 0 120.37303
Loop time of 0.405054 on 4 procs for 100 steps with 21 atoms
Performance: 21.331 ns/day, 1.125 hours/ns, 246.881 timesteps/s
96.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.16194 | 0.24674 | 0.40012 | 18.4 | 60.92
Neigh | 7.3671e-05 | 0.00024015 | 0.00053477 | 1.1 | 0.06
Comm | 0.0037704 | 0.1575 | 0.24247 | 23.1 | 38.88
Output | 0.00037122 | 0.00040913 | 0.0004406 | 0.1 | 0.10
Modify | 4.22e-05 | 6.175e-05 | 8.3685e-05 | 0.2 | 0.02
Other | | 0.0001087 | | | 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

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LAMMPS (5 Oct 2016)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
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
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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 atom 10 dump.reaxc.rdx
#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 ...
2 neighbor list requests
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
Memory usage per processor = 14.4462 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 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068717 0.2433807 0 96.181613 0.96184887 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961
Loop time of 0.362895 on 1 procs for 100 steps with 21 atoms
Performance: 23.809 ns/day, 1.008 hours/ns, 275.562 timesteps/s
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 | 0.34367 | 0.34367 | 0.34367 | 0.0 | 94.70
Neigh | 0.0078354 | 0.0078354 | 0.0078354 | 0.0 | 2.16
Comm | 0.00043559 | 0.00043559 | 0.00043559 | 0.0 | 0.12
Output | 0.00019908 | 0.00019908 | 0.00019908 | 0.0 | 0.05
Modify | 0.010645 | 0.010645 | 0.010645 | 0.0 | 2.93
Other | | 0.0001094 | | | 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: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.1905
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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LAMMPS (5 Oct 2016)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
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
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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 atom 10 dump.reaxc.rdx
#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 ...
2 neighbor list requests
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
Memory usage per processor = 12.531 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 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418
10 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252288 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
20 538.95831 -1942.7037 -1910.5731 -10725.671 -2803.7395 7.9078306 0.077926651 0 81.610051 0.22951926 -57.557099 0 30.331204 -10.178049 878.99014 -159.69268 0 89.316921
30 463.09502 -1933.5765 -1905.9685 -33255.512 -2749.8591 -8.015455 0.027628766 0 81.6274 0.11972393 -50.262275 0 20.820315 -9.6327041 851.88722 -149.49498 0 79.205714
40 885.49378 -1958.9125 -1906.1228 -4814.644 -2795.644 9.1506485 0.13747497 0 70.948 0.24360511 -57.862677 0 19.076502 -11.141216 873.73898 -159.99393 0 92.43409
50 861.16297 -1954.4602 -1903.1209 -1896.8002 -2784.8451 3.8270162 0.157933 0 79.851673 3.3492148 -78.066132 0 32.628944 -7.9565368 872.81852 -190.98572 0 114.76001
60 1167.7835 -1971.8433 -1902.2245 -3482.8296 -2705.8635 -17.121613 0.2274909 0 44.507674 7.85602 -74.788998 0 16.256483 -4.6046575 835.83058 -188.33691 0 114.19414
70 1439.9939 -1989.3026 -1903.4556 23846.042 -2890.7893 31.958672 0.26671708 0 85.758381 3.1804035 -71.002944 0 24.357195 -10.311284 905.8679 -175.38487 0 106.79661
80 502.39535 -1930.7548 -1900.8039 -20356.194 -2703.8126 -18.662209 0.11286005 0 99.803849 2.0329206 -76.171278 0 19.23716 -6.2787147 826.47505 -166.03123 0 92.539386
90 749.07874 -1946.9841 -1902.3269 17798.394 -2863.7576 42.068612 0.24338059 0 96.181423 0.96185061 -69.95542 0 24.615344 -11.582758 903.68812 -190.13826 0 120.69124
100 1109.6904 -1968.5879 -1902.4323 -4490.0667 -2755.8991 -7.1224194 0.21757691 0 61.805857 7.0827218 -75.645383 0 20.115437 -6.23727 863.56487 -198.56975 0 122.09963
Loop time of 0.293673 on 4 procs for 100 steps with 21 atoms
Performance: 29.420 ns/day, 0.816 hours/ns, 340.514 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24143 | 0.24223 | 0.24409 | 0.2 | 82.48
Neigh | 0.003767 | 0.0049117 | 0.0061524 | 1.2 | 1.67
Comm | 0.0030656 | 0.0048578 | 0.0057402 | 1.5 | 1.65
Output | 0.00033545 | 0.00036347 | 0.00038052 | 0.1 | 0.12
Modify | 0.039885 | 0.041207 | 0.042435 | 0.4 | 14.03
Other | | 0.0001001 | | | 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: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1195
Ave neighs/atom = 56.9048
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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 Normal file
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@ -0,0 +1,107 @@
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

46
examples/reax/log.5Oct16.reax.tatb.g++.1 → examples/reax/log.8March18.reax.tatb.g++.1
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system # ReaxFF potential for TATB system
units real units real
@ -12,7 +13,7 @@ read_data data.tatb
# reax args: hbcut hbnewflag tripflag precision # reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6 pair_style reax 6.0 1 1 1.0e-6
WARNING: The pair_style reax command will be deprecated soon - users should switch to pair_style reax/c (../pair_reax.cpp:49) 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 pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax compute reax all pair reax
@ -54,34 +55,39 @@ fix 2 all reax/bonds 25 bonds.reax.tatb
run 25 run 25
Neighbor list info ... Neighbor list info ...
1 neighbor list requests
update every 5 steps, delay 0 steps, check no update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5 master list distance cutoff = 12.5
ghost atom cutoff = 12.5 ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 4 3 binsize = 6.25, bins = 5 4 3
Memory usage per processor = 6.61277 Mbytes 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 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 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 0.63682807 -44767.737 -44767.01 8391.5966 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2727 0 6388.8127 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 2.4306957 -44769.41 -44766.635 11717.369 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0713 0 6381.7946 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 5.0590478 -44772.63 -44766.854 17125.033 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3112 0 6370.4665 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 8.0678579 -44775.923 -44766.713 24620.824 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3104 0 6355.1097 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 10.975539 -44777.231 -44764.701 34381.278 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.2311 -1582.8552 253.88696 -653.46042 18790.855 -8683.8362 0 6336.3099 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 7.48375 on 1 procs for 25 steps with 384 atoms Loop time of 7.80129 on 1 procs for 25 steps with 384 atoms
Performance: 0.018 ns/day, 1330.444 hours/ns, 3.341 timesteps/s Performance: 0.017 ns/day, 1386.896 hours/ns, 3.205 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 7.4284 | 7.4284 | 7.4284 | 0.0 | 99.26 Pair | 7.7384 | 7.7384 | 7.7384 | 0.0 | 99.19
Neigh | 0.051549 | 0.051549 | 0.051549 | 0.0 | 0.69 Neigh | 0.058615 | 0.058615 | 0.058615 | 0.0 | 0.75
Comm | 0.0021887 | 0.0021887 | 0.0021887 | 0.0 | 0.03 Comm | 0.0022428 | 0.0022428 | 0.0022428 | 0.0 | 0.03
Output | 0.00025821 | 0.00025821 | 0.00025821 | 0.0 | 0.00 Output | 0.00033212 | 0.00033212 | 0.00033212 | 0.0 | 0.00
Modify | 0.00099206 | 0.00099206 | 0.00099206 | 0.0 | 0.01 Modify | 0.0013618 | 0.0013618 | 0.0013618 | 0.0 | 0.02
Other | | 0.0003154 | | | 0.00 Other | | 0.0003309 | | | 0.00
Nlocal: 384 ave 384 max 384 min Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -94,4 +100,4 @@ Total # of neighbors = 286828
Ave neighs/atom = 746.948 Ave neighs/atom = 746.948
Neighbor list builds = 5 Neighbor list builds = 5
Dangerous builds not checked Dangerous builds not checked
Total wall time: 0:00:07 Total wall time: 0:00:08

44
examples/reax/log.5Oct16.reax.tatb.g++.4 → examples/reax/log.8March18.reax.tatb.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system # ReaxFF potential for TATB system
units real units real
@ -12,7 +13,7 @@ read_data data.tatb
# reax args: hbcut hbnewflag tripflag precision # reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6 pair_style reax 6.0 1 1 1.0e-6
WARNING: The pair_style reax command will be deprecated soon - users should switch to pair_style reax/c (../pair_reax.cpp:49) 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 pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax compute reax all pair reax
@ -54,34 +55,39 @@ fix 2 all reax/bonds 25 bonds.reax.tatb
run 25 run 25
Neighbor list info ... Neighbor list info ...
1 neighbor list requests
update every 5 steps, delay 0 steps, check no update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5 master list distance cutoff = 12.5
ghost atom cutoff = 12.5 ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 4 3 binsize = 6.25, bins = 5 4 3
Memory usage per processor = 4.03843 Mbytes 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 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 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 0.63682726 -44767.816 -44767.089 8391.165 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3995 0 6388.86 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 2.4306905 -44769.408 -44766.633 11717.247 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.0965 0 6381.8216 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 5.0590422 -44772.626 -44766.85 17124.943 -61103.34 489.2801 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3383 0 6370.4973 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 8.0678512 -44775.934 -44766.723 24620.531 -61088.791 490.42349 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.4033 0 6355.1921 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 10.97553 -44777.231 -44764.701 34381.242 -61068.889 490.53154 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.8451 0 6336.3185 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 3.27945 on 4 procs for 25 steps with 384 atoms Loop time of 3.74388 on 4 procs for 25 steps with 384 atoms
Performance: 0.041 ns/day, 583.013 hours/ns, 7.623 timesteps/s Performance: 0.036 ns/day, 665.579 hours/ns, 6.678 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads 98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 3.0329 | 3.1456 | 3.2612 | 5.2 | 95.92 Pair | 3.478 | 3.6025 | 3.7215 | 4.8 | 96.22
Neigh | 0.011087 | 0.011261 | 0.011608 | 0.2 | 0.34 Neigh | 0.012731 | 0.01299 | 0.013174 | 0.2 | 0.35
Comm | 0.0057111 | 0.12121 | 0.23398 | 26.2 | 3.70 Comm | 0.0073411 | 0.12653 | 0.25119 | 25.4 | 3.38
Output | 0.00039172 | 0.0005855 | 0.00080633 | 0.6 | 0.02 Output | 0.00050354 | 0.00081849 | 0.0011628 | 0.0 | 0.02
Modify | 0.00035787 | 0.00059456 | 0.00082469 | 0.7 | 0.02 Modify | 0.00049281 | 0.00082356 | 0.001157 | 0.0 | 0.02
Other | | 0.0002265 | | | 0.01 Other | | 0.0002663 | | | 0.01
Nlocal: 96 ave 96 max 96 min Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0

115
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@ -0,0 +1,115 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
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
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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 atom 10 dump.reaxc.rdx
#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
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 15.28 | 15.28 | 15.28 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 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79937 0 168.88402
10 1288.6114 -1989.6644 -1912.8422 -19456.35 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252294 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43322 0 107.75935
20 538.95849 -1942.7037 -1910.5731 -10725.658 -2803.7395 7.9078331 0.077926702 0 81.610043 0.22951937 -57.557104 0 30.331203 -10.178049 878.99015 -159.69092 0 89.315159
30 463.09542 -1933.5765 -1905.9685 -33255.507 -2749.8591 -8.0154628 0.027628767 0 81.627403 0.11972403 -50.262284 0 20.82032 -9.6327022 851.88722 -149.495 0 79.205731
40 885.49449 -1958.9126 -1906.1228 -4814.7123 -2795.644 9.1506221 0.1374749 0 70.948046 0.24360579 -57.8627 0 19.076515 -11.141211 873.73892 -159.9939 0 92.434059
50 861.1646 -1954.4599 -1903.1206 -1896.7387 -2784.8446 3.8269113 0.1579328 0 79.851775 3.3492107 -78.066127 0 32.628975 -7.9565255 872.81826 -190.98565 0 114.75994
60 1167.785 -1971.8432 -1902.2243 -3482.6975 -2705.8638 -17.121582 0.22749067 0 44.507705 7.856069 -74.788959 0 16.256519 -4.6046602 835.8308 -188.33691 0 114.19414
70 1439.9947 -1989.3024 -1903.4554 23845.067 -2890.7896 31.958874 0.26671735 0 85.758608 3.1803486 -71.002907 0 24.357106 -10.311315 905.86799 -175.38482 0 106.79659
80 502.40024 -1930.7547 -1900.8035 -20356.557 -2703.8096 -18.663105 0.11286226 0 99.803799 2.0329394 -76.171387 0 19.236609 -6.2786041 826.47358 -166.03157 0 92.539694
90 749.09267 -1946.9834 -1902.3254 17798.812 -2863.7586 42.068927 0.24338042 0 96.18195 0.96181754 -69.955528 0 24.61541 -11.58277 903.68895 -190.13838 0 120.69139
100 1109.7046 -1968.5875 -1902.4311 -4490.6736 -2755.8953 -7.1235173 0.21757663 0 61.806405 7.0825933 -75.645487 0 20.114745 -6.2371664 863.56285 -198.56939 0 122.09923
Loop time of 0.395195 on 1 procs for 100 steps with 21 atoms
Performance: 21.863 ns/day, 1.098 hours/ns, 253.039 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.3722 | 0.3722 | 0.3722 | 0.0 | 94.18
Neigh | 0.0098455 | 0.0098455 | 0.0098455 | 0.0 | 2.49
Comm | 0.00047445 | 0.00047445 | 0.00047445 | 0.0 | 0.12
Output | 0.00034022 | 0.00034022 | 0.00034022 | 0.0 | 0.09
Modify | 0.012187 | 0.012187 | 0.012187 | 0.0 | 3.08
Other | | 0.0001521 | | | 0.04
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: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.1905
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

115
examples/reax/log.8March18.reaxc.rdx.g++.4 Normal file
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@ -0,0 +1,115 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
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
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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 atom 10 dump.reaxc.rdx
#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
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.37 | 11.76 | 13.34 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 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79988 0 168.88453
10 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252286 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934
20 538.95818 -1942.7037 -1910.5731 -10725.623 -2803.7394 7.9078307 0.077926702 0 81.61005 0.22951942 -57.557107 0 30.331206 -10.178049 878.9901 -159.68951 0 89.313749
30 463.09514 -1933.5765 -1905.9685 -33255.525 -2749.859 -8.0154737 0.027628797 0 81.627408 0.11972402 -50.262283 0 20.82031 -9.6327021 851.88715 -149.49499 0 79.205724
40 885.49412 -1958.9125 -1906.1227 -4814.6606 -2795.6439 9.150622 0.13747487 0 70.948029 0.24360517 -57.862679 0 19.076509 -11.141214 873.7389 -159.99392 0 92.434078
50 861.16393 -1954.46 -1903.1207 -1896.7323 -2784.8449 3.8270197 0.1579328 0 79.851743 3.3492115 -78.066132 0 32.628992 -7.9565379 872.81841 -190.98568 0 114.75996
60 1167.7846 -1971.8432 -1902.2243 -3482.8111 -2705.8633 -17.121657 0.2274907 0 44.507681 7.8560366 -74.788989 0 16.256493 -4.6046537 835.8305 -188.33687 0 114.1941
70 1439.9942 -1989.3023 -1903.4554 23845.444 -2890.7894 31.958784 0.26671721 0 85.758586 3.1803655 -71.002918 0 24.357158 -10.311304 905.86792 -175.38481 0 106.79657
80 502.3975 -1930.7546 -1900.8036 -20356.439 -2703.8105 -18.662812 0.11286123 0 99.80391 2.0329293 -76.171334 0 19.236803 -6.2786439 826.47397 -166.03141 0 92.539551
90 749.09048 -1946.9837 -1902.3258 17798.718 -2863.7582 42.068719 0.24338057 0 96.181773 0.96183581 -69.955529 0 24.615414 -11.582758 903.68862 -190.1384 0 120.69139
100 1109.6999 -1968.5875 -1902.4314 -4490.3728 -2755.8964 -7.1231468 0.21757685 0 61.806149 7.0826648 -75.645428 0 20.115002 -6.2371958 863.56343 -198.56957 0 122.09942
Loop time of 0.329552 on 4 procs for 100 steps with 21 atoms
Performance: 26.217 ns/day, 0.915 hours/ns, 303.443 timesteps/s
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26372 | 0.26499 | 0.26754 | 0.3 | 80.41
Neigh | 0.0045478 | 0.0062494 | 0.0076699 | 1.5 | 1.90
Comm | 0.0041637 | 0.0064691 | 0.0080271 | 1.8 | 1.96
Output | 0.00054169 | 0.00056636 | 0.00060368 | 0.0 | 0.17
Modify | 0.049433 | 0.051134 | 0.05311 | 0.6 | 15.52
Other | | 0.000141 | | | 0.04
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: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1195
Ave neighs/atom = 56.9048
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

51
examples/reax/log.5Oct16.reaxc.tatb.g++.1 → examples/reax/log.8March18.reaxc.tatb.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system # ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb, # this run is equivalent to reax/in.reax.tatb,
@ -56,34 +57,44 @@ fix 3 all reax/c/species 1 5 5 species.tatb
run 25 run 25
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 5 steps, delay 0 steps, check no update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5 master list distance cutoff = 12.5
ghost atom cutoff = 12.5 ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 4 3 binsize = 6.25, bins = 5 4 3
Memory usage per processor = 155.82 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 176.7 | 176.7 | 176.7 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 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 -44760.998 -44760.998 7827.7879 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274 0 0 -44760.998 -44760.998 7827.7874 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6395 0 6391.0275
5 0.61603942 -44761.698 -44760.994 8934.6281 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691 5 0.61603968 -44761.698 -44760.994 8934.6347 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671
10 2.3525551 -44763.227 -44760.541 12288.607 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9688 0 6381.7066 10 2.3525551 -44763.227 -44760.541 12288.583 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9768 0 6381.7146
15 4.9013326 -44766.36 -44760.764 17717.015 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.237 0 6370.4033 15 4.9013279 -44766.36 -44760.764 17717.01 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2375 0 6370.4038
20 7.829471 -44769.686 -44760.747 25205.558 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5091 0 6355.2604 20 7.8294645 -44769.686 -44760.747 25205.624 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4889 0 6355.2402
25 10.697926 -44772.904 -44760.691 34232.793 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3608 0 6336.8416 25 10.697904 -44772.904 -44760.691 34232.965 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3125 0 6336.7934
Loop time of 4.34725 on 1 procs for 25 steps with 384 atoms Loop time of 4.72562 on 1 procs for 25 steps with 384 atoms
Performance: 0.031 ns/day, 772.845 hours/ns, 5.751 timesteps/s Performance: 0.029 ns/day, 840.110 hours/ns, 5.290 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 3.5264 | 3.5264 | 3.5264 | 0.0 | 81.12 Pair | 3.775 | 3.775 | 3.775 | 0.0 | 79.88
Neigh | 0.40335 | 0.40335 | 0.40335 | 0.0 | 9.28 Neigh | 0.47047 | 0.47047 | 0.47047 | 0.0 | 9.96
Comm | 0.0021031 | 0.0021031 | 0.0021031 | 0.0 | 0.05 Comm | 0.0025151 | 0.0025151 | 0.0025151 | 0.0 | 0.05
Output | 0.00019765 | 0.00019765 | 0.00019765 | 0.0 | 0.00 Output | 0.0003159 | 0.0003159 | 0.0003159 | 0.0 | 0.01
Modify | 0.41479 | 0.41479 | 0.41479 | 0.0 | 9.54 Modify | 0.47676 | 0.47676 | 0.47676 | 0.0 | 10.09
Other | | 0.0004084 | | | 0.01 Other | | 0.0005293 | | | 0.01
Nlocal: 384 ave 384 max 384 min Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -99,4 +110,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04 Total wall time: 0:00:05

51
examples/reax/log.5Oct16.reaxc.tatb.g++.4 → examples/reax/log.8March18.reaxc.tatb.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system # ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb, # this run is equivalent to reax/in.reax.tatb,
@ -56,34 +57,44 @@ fix 3 all reax/c/species 1 5 5 species.tatb
run 25 run 25
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 5 steps, delay 0 steps, check no update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5 master list distance cutoff = 12.5
ghost atom cutoff = 12.5 ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 4 3 binsize = 6.25, bins = 5 4 3
Memory usage per processor = 105.386 Mbytes 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 118 | 118 | 118 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 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 -44760.998 -44760.998 7827.7867 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277 0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277
5 0.61603967 -44761.698 -44760.994 8934.6339 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1905 0 6388.6665 5 0.61603968 -44761.698 -44760.994 8934.6335 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666
10 2.3525545 -44763.227 -44760.541 12288.586 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.714 10 2.3525544 -44763.227 -44760.541 12288.587 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9764 0 6381.7141
15 4.9013281 -44766.36 -44760.764 17716.982 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2476 0 6370.4138 15 4.9013311 -44766.36 -44760.764 17716.955 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2558 0 6370.4221
20 7.8294637 -44769.686 -44760.747 25205.512 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.518 0 6355.2692 20 7.8294715 -44769.686 -44760.747 25205.613 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4906 0 6355.2419
25 10.697905 -44772.904 -44760.691 34232.815 -61069.308 490.25887 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3481 0 6336.829 25 10.697924 -44772.904 -44760.691 34232.794 -61069.308 490.25886 4.7163736 0 1570.7397 20.181347 -251.91376 -1582.3261 253.82253 -653.53183 18791.975 -8684.3641 0 6336.8449
Loop time of 2.60733 on 4 procs for 25 steps with 384 atoms Loop time of 2.84068 on 4 procs for 25 steps with 384 atoms
Performance: 0.052 ns/day, 463.526 hours/ns, 9.588 timesteps/s Performance: 0.048 ns/day, 505.009 hours/ns, 8.801 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads 98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 2.1835 | 2.1843 | 2.1854 | 0.0 | 83.77 Pair | 2.3253 | 2.328 | 2.3305 | 0.2 | 81.95
Neigh | 0.22091 | 0.22364 | 0.22821 | 0.6 | 8.58 Neigh | 0.2589 | 0.26458 | 0.26897 | 0.7 | 9.31
Comm | 0.005677 | 0.0069622 | 0.0078082 | 1.0 | 0.27 Comm | 0.0094428 | 0.012062 | 0.014872 | 2.3 | 0.42
Output | 0.00036621 | 0.0028675 | 0.0037034 | 2.7 | 0.11 Output | 0.00043392 | 0.0042209 | 0.0054941 | 3.4 | 0.15
Modify | 0.18736 | 0.18921 | 0.19102 | 0.4 | 7.26 Modify | 0.22563 | 0.23134 | 0.23579 | 0.8 | 8.14
Other | | 0.0003636 | | | 0.01 Other | | 0.0005122 | | | 0.02
Nlocal: 96 ave 96 max 96 min Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
@ -99,4 +110,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02 Total wall time: 0:00:03