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update log files for airebo and atm examples

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This commit is contained in:
Axel Kohlmeyer
2018-11-28 14:28:20 -05:00
parent c0ab126e77
commit 77e7362168
11 changed files with 120 additions and 112 deletions
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1
examples/airebo/CH.airebo Symbolic link
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../../potentials/CH.airebo

1
examples/airebo/CH.airebo-m Symbolic link
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../../potentials/CH.airebo-m

26
examples/airebo/in.airebo
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# AIREBO polyethelene benchmark
units metal
atom_style atomic
units metal
atom_style atomic
read_data data.airebo
read_data data.airebo
replicate 17 16 2
replicate 17 16 2
neighbor 0.5 bin
neigh_modify delay 5 every 1
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * ../../potentials/CH.airebo C H
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
fix 1 all nve
timestep 0.0005
thermo 10
run 100
thermo 10
run 100

26
examples/airebo/in.airebo-m
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@ -1,22 +1,22 @@
# AIREBO polyethelene benchmark
units metal
atom_style atomic
units metal
atom_style atomic
read_data data.airebo
read_data data.airebo
replicate 17 16 2
replicate 17 16 2
neighbor 0.5 bin
neigh_modify delay 5 every 1
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo/morse 3.0 1 1
pair_coeff * * ../../potentials/CH.airebo-m C H
pair_style airebo/morse 3.0 1 1
pair_coeff * * CH.airebo-m C H
velocity all create 300.0 761341
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
fix 1 all nve
timestep 0.0005
thermo 10
run 100
thermo 10
run 100

23
examples/airebo/log.23Jun17.airebo-m.g++.1 → examples/airebo/log.27Nov18.airebo-m.g++.1
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@ -1,4 +1,4 @@
LAMMPS (23 Jun 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
@ -15,6 +15,7 @@ replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00141144 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -55,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press
80 164.28396 -138709.5 0 -138016.4 -1524.7353
90 180.26403 -138776.42 0 -138015.9 -27143.467
100 164.05694 -138706.58 0 -138014.44 5157.5516
Loop time of 117.672 on 1 procs for 100 steps with 32640 atoms
Loop time of 64.6107 on 1 procs for 100 steps with 32640 atoms
Performance: 0.037 ns/day, 653.734 hours/ns, 0.850 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.067 ns/day, 358.948 hours/ns, 1.548 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 108.31 | 108.31 | 108.31 | 0.0 | 92.04
Neigh | 9.2199 | 9.2199 | 9.2199 | 0.0 | 7.84
Comm | 0.052942 | 0.052942 | 0.052942 | 0.0 | 0.04
Output | 0.0015149 | 0.0015149 | 0.0015149 | 0.0 | 0.00
Modify | 0.060962 | 0.060962 | 0.060962 | 0.0 | 0.05
Other | | 0.02656 | | | 0.02
Pair | 59.916 | 59.916 | 59.916 | 0.0 | 92.73
Neigh | 4.6347 | 4.6347 | 4.6347 | 0.0 | 7.17
Comm | 0.025572 | 0.025572 | 0.025572 | 0.0 | 0.04
Output | 0.00098896 | 0.00098896 | 0.00098896 | 0.0 | 0.00
Modify | 0.022327 | 0.022327 | 0.022327 | 0.0 | 0.03
Other | | 0.01076 | | | 0.02
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -83,4 +84,4 @@ Total # of neighbors = 22210922
Ave neighs/atom = 680.482
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:02:00
Total wall time: 0:01:05

23
examples/airebo/log.23Jun17.airebo-m.g++.4 → examples/airebo/log.27Nov18.airebo-m.g++.4
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@ -1,4 +1,4 @@
LAMMPS (23 Jun 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
@ -15,6 +15,7 @@ replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.000637531 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -55,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press
80 164.28396 -138709.5 0 -138016.4 -1524.7353
90 180.26403 -138776.42 0 -138015.9 -27143.467
100 164.05694 -138706.58 0 -138014.44 5157.5516
Loop time of 32.9268 on 4 procs for 100 steps with 32640 atoms
Loop time of 18.1922 on 4 procs for 100 steps with 32640 atoms
Performance: 0.131 ns/day, 182.927 hours/ns, 3.037 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.237 ns/day, 101.068 hours/ns, 5.497 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 28.045 | 28.537 | 29.42 | 10.4 | 86.67
Neigh | 3.163 | 3.237 | 3.3761 | 4.7 | 9.83
Comm | 0.09883 | 1.1206 | 1.6862 | 60.4 | 3.40
Output | 0.00099325 | 0.0011329 | 0.0012462 | 0.3 | 0.00
Modify | 0.016013 | 0.016726 | 0.017257 | 0.4 | 0.05
Other | | 0.01459 | | | 0.04
Pair | 15.968 | 16.084 | 16.308 | 3.4 | 88.41
Neigh | 1.6017 | 1.6334 | 1.7006 | 3.1 | 8.98
Comm | 0.1603 | 0.45122 | 0.59951 | 26.0 | 2.48
Output | 0.00042605 | 0.00073195 | 0.0016003 | 0.0 | 0.00
Modify | 0.0092106 | 0.010544 | 0.014411 | 2.2 | 0.06
Other | | 0.01193 | | | 0.07
Nlocal: 8160 ave 8167 max 8153 min
Histogram: 1 0 1 0 0 0 0 1 0 1
@ -83,4 +84,4 @@ Total # of neighbors = 22210922
Ave neighs/atom = 680.482
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:33
Total wall time: 0:00:18

23
examples/airebo/log.23Jun17.airebo.g++.1 → examples/airebo/log.27Nov18.airebo.g++.1
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@ -1,4 +1,4 @@
LAMMPS (23 Jun 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
@ -15,6 +15,7 @@ replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00144172 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -55,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press
80 157.16184 -138695.77 0 -138032.72 19824.698
90 196.15907 -138860.65 0 -138033.07 -7950.8462
100 178.31875 -138784.89 0 -138032.57 30997.671
Loop time of 110.107 on 1 procs for 100 steps with 32640 atoms
Loop time of 57.9914 on 1 procs for 100 steps with 32640 atoms
Performance: 0.039 ns/day, 611.705 hours/ns, 0.908 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.074 ns/day, 322.174 hours/ns, 1.724 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 100.76 | 100.76 | 100.76 | 0.0 | 91.51
Neigh | 9.1909 | 9.1909 | 9.1909 | 0.0 | 8.35
Comm | 0.058134 | 0.058134 | 0.058134 | 0.0 | 0.05
Output | 0.0015941 | 0.0015941 | 0.0015941 | 0.0 | 0.00
Modify | 0.062212 | 0.062212 | 0.062212 | 0.0 | 0.06
Other | | 0.03123 | | | 0.03
Pair | 53.275 | 53.275 | 53.275 | 0.0 | 91.87
Neigh | 4.6548 | 4.6548 | 4.6548 | 0.0 | 8.03
Comm | 0.026622 | 0.026622 | 0.026622 | 0.0 | 0.05
Output | 0.00097251 | 0.00097251 | 0.00097251 | 0.0 | 0.00
Modify | 0.022773 | 0.022773 | 0.022773 | 0.0 | 0.04
Other | | 0.01089 | | | 0.02
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -83,4 +84,4 @@ Total # of neighbors = 22217840
Ave neighs/atom = 680.694
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:01:52
Total wall time: 0:00:59

23
examples/airebo/log.23Jun17.airebo.g++.4 → examples/airebo/log.27Nov18.airebo.g++.4
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@ -1,4 +1,4 @@
LAMMPS (23 Jun 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
@ -15,6 +15,7 @@ replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.00262594 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -55,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press
80 157.16184 -138695.77 0 -138032.72 19824.698
90 196.15907 -138860.65 0 -138033.07 -7950.8462
100 178.31875 -138784.89 0 -138032.57 30997.671
Loop time of 30.1916 on 4 procs for 100 steps with 32640 atoms
Loop time of 16.4395 on 4 procs for 100 steps with 32640 atoms
Performance: 0.143 ns/day, 167.731 hours/ns, 3.312 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.263 ns/day, 91.331 hours/ns, 6.083 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 26.083 | 26.31 | 26.795 | 5.5 | 87.14
Neigh | 3.1781 | 3.2134 | 3.2775 | 2.2 | 10.64
Comm | 0.086296 | 0.63643 | 0.88995 | 40.2 | 2.11
Output | 0.00074124 | 0.0010698 | 0.0013616 | 0.7 | 0.00
Modify | 0.015335 | 0.016373 | 0.017565 | 0.8 | 0.05
Other | | 0.01457 | | | 0.05
Pair | 14.263 | 14.349 | 14.483 | 2.3 | 87.28
Neigh | 1.6071 | 1.6283 | 1.6636 | 1.7 | 9.90
Comm | 0.26261 | 0.43435 | 0.52323 | 16.1 | 2.64
Output | 0.00042105 | 0.0007121 | 0.001538 | 0.0 | 0.00
Modify | 0.00898 | 0.009112 | 0.0093675 | 0.2 | 0.06
Other | | 0.0184 | | | 0.11
Nlocal: 8160 ave 8174 max 8146 min
Histogram: 1 0 1 0 0 0 0 1 0 1
@ -83,4 +84,4 @@ Total # of neighbors = 22217840
Ave neighs/atom = 680.694
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:30
Total wall time: 0:00:16

40
examples/atm/in.atm
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@ -1,31 +1,31 @@
# Axilrod-Teller-Muto potential example
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 10*$x
variable yy equal 10*$y
variable zz equal 10*$z
variable xx equal 10*$x
variable yy equal 10*$y
variable zz equal 10*$z
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.65
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 0.65
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * atm * 0.072
pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * atm * 0.072
mass * 1.0
velocity all create 1.033 12345678 loop geom
mass * 1.0
velocity all create 1.033 12345678 loop geom
fix 1 all nvt temp 1.033 1.033 0.05
fix 1 all nvt temp 1.033 1.033 0.05
timestep 0.002
thermo 5
thermo 5
run 25
run 25

23
examples/atm/log.27Aug18.g++.1 → examples/atm/log.27Nov18.atm.g++.1
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@ -1,4 +1,5 @@
LAMMPS (22 Aug 2018)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Axilrod-Teller-Muto potential example
variable x index 1
@ -26,7 +27,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.00139618 secs
Time spent = 0.000354767 secs
pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
@ -66,20 +67,20 @@ Step Temp E_pair E_mol TotEng Press
15 1.0376519 -4.84599 0 -3.2899013 -4.0278711
20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052
25 1.0347886 -4.84473 0 -3.2929351 -3.8044469
Loop time of 15.95 on 1 procs for 25 steps with 4000 atoms
Loop time of 11.3218 on 1 procs for 25 steps with 4000 atoms
Performance: 270.846 tau/day, 1.567 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 381.565 tau/day, 2.208 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.946 | 15.946 | 15.946 | 0.0 | 99.97
Pair | 11.319 | 11.319 | 11.319 | 0.0 | 99.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0015042 | 0.0015042 | 0.0015042 | 0.0 | 0.01
Output | 0.00013781 | 0.00013781 | 0.00013781 | 0.0 | 0.00
Modify | 0.0017776 | 0.0017776 | 0.0017776 | 0.0 | 0.01
Other | | 0.0006771 | | | 0.00
Comm | 0.0010235 | 0.0010235 | 0.0010235 | 0.0 | 0.01
Output | 0.00010943 | 0.00010943 | 0.00010943 | 0.0 | 0.00
Modify | 0.0012162 | 0.0012162 | 0.0012162 | 0.0 | 0.01
Other | | 0.0004497 | | | 0.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -97,4 +98,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:16
Total wall time: 0:00:11

23
examples/atm/log.27Aug18.g++.4 → examples/atm/log.27Nov18.atm.g++.4
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@ -1,4 +1,5 @@
LAMMPS (22 Aug 2018)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Axilrod-Teller-Muto potential example
variable x index 1
@ -26,7 +27,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000900984 secs
Time spent = 0.000210762 secs
pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
@ -66,20 +67,20 @@ Step Temp E_pair E_mol TotEng Press
15 1.0376519 -4.84599 0 -3.2899013 -4.0278711
20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052
25 1.0347886 -4.84473 0 -3.2929351 -3.8044469
Loop time of 4.34636 on 4 procs for 25 steps with 4000 atoms
Loop time of 2.95263 on 4 procs for 25 steps with 4000 atoms
Performance: 993.935 tau/day, 5.752 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 1463.102 tau/day, 8.467 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.9977 | 4.1036 | 4.209 | 4.9 | 94.41
Pair | 2.8823 | 2.9082 | 2.9447 | 1.4 | 98.49
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.13588 | 0.24134 | 0.34722 | 20.4 | 5.55
Output | 0.00013757 | 0.00015104 | 0.00016761 | 0.0 | 0.00
Modify | 0.00087953 | 0.00091547 | 0.00095582 | 0.0 | 0.02
Other | | 0.0003656 | | | 0.01
Comm | 0.0066586 | 0.043249 | 0.069202 | 11.8 | 1.46
Output | 7.3671e-05 | 0.00015199 | 0.00038099 | 0.0 | 0.01
Modify | 0.00061488 | 0.0006243 | 0.00063872 | 0.0 | 0.02
Other | | 0.0004148 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -97,4 +98,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04
Total wall time: 0:00:03