Commit 98c8f220 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

update log files for coreshell examples

parent 296cab0b

examples/coreshell/log.9Nov16.coreshell.dsf.g++.1→examples/coreshell/log.27Nov18.coreshell.dsf.g++.1

+32 −26
Original line number Diff line number Diff line 
LAMMPS (27 Oct 2016)

LAMMPS (27 Nov 2018)

  using 1 OpenMP thread(s) per MPI task

# Testsystem for core-shell model compared to Mitchel and Finchham

# Hendrik Heenen, June 2014
@@ -68,12 +69,17 @@ thermo_modify temp CSequ 


velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 22

  ghost atom cutoff = 22

  binsize = 11 -> bins = 3 3 3

  binsize = 11, bins = 3 3 3

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair born/coul/dsf/cs, perpetual

      attributes: half, newton on

      pair build: half/bin/newton

      stencil: half/bin/3d/newton

      bin: standard

velocity all scale 1427 temp CSequ



fix thermoberendsen all temp/berendsen 1427 1427 0.4
@@ -84,7 +90,7 @@ fix_modify thermoberendsen temp CSequ 


timestep 0.002

run 500

Memory usage per processor = 7.04355 Mbytes

Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes

Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 

       0   -635.80596   -675.46362    39.657659         1427   -21302.622   -675.46362    1.6320365   -677.09565            0            0 1.3517686e-14 2.942091e-15      13990.5 

      50    -633.9898   -666.02679     32.03699    1152.7858   -4578.5681   -668.50431    37.800204   -706.30452            0    2.4775226    14.568073    4.3012389      13990.5
@@ -97,21 +103,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm 
     400   -625.02586   -661.46042    36.434568    1311.0236    -868.2031   -664.40231     43.21398   -707.61629            0    2.9418875    14.945389    2.7493413      13990.5 

     450    -624.3278   -660.50844    36.180639    1301.8865   -2203.3944   -663.49896    40.008669   -703.50763            0    2.9905179    14.158866    1.7299899      13990.5 

     500   -623.56254   -661.33839    37.775849    1359.2869   -810.50736   -664.11652    42.993999   -707.11052            0    2.7781274     13.68709    2.9115277      13990.5 

Loop time of 10.7162 on 1 procs for 500 steps with 432 atoms

Loop time of 8.43387 on 1 procs for 500 steps with 432 atoms



Performance: 8.063 ns/day, 2.977 hours/ns, 46.658 timesteps/s

99.9% CPU use with 1 MPI tasks x no OpenMP threads

Performance: 10.244 ns/day, 2.343 hours/ns, 59.285 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    | 10.478     | 10.478     | 10.478     |   0.0 | 97.78

Bond    | 0.0029511  | 0.0029511  | 0.0029511  |   0.0 |  0.03

Neigh   | 0.14159    | 0.14159    | 0.14159    |   0.0 |  1.32

Comm    | 0.074382   | 0.074382   | 0.074382   |   0.0 |  0.69

Output  | 0.00054097 | 0.00054097 | 0.00054097 |   0.0 |  0.01

Modify  | 0.010588   | 0.010588   | 0.010588   |   0.0 |  0.10

Other   |            | 0.007748   |            |       |  0.07

Pair    | 8.1175     | 8.1175     | 8.1175     |   0.0 | 96.25

Bond    | 0.0019796  | 0.0019796  | 0.0019796  |   0.0 |  0.02

Neigh   | 0.21242    | 0.21242    | 0.21242    |   0.0 |  2.52

Comm    | 0.085533   | 0.085533   | 0.085533   |   0.0 |  1.01

Output  | 0.00041103 | 0.00041103 | 0.00041103 |   0.0 |  0.00

Modify  | 0.012187   | 0.012187   | 0.012187   |   0.0 |  0.14

Other   |            | 0.003863   |            |       |  0.05



Nlocal:    432 ave 432 max 432 min

Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -131,7 +137,7 @@ unfix thermoberendsen 
# ------------------------ Dynamic Run -------------------------------



run 1000

Memory usage per processor = 7.04355 Mbytes

Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes

Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 

     500   -623.56254   -661.33839    37.775849    1359.2869   -810.50736   -664.11652    42.993999   -707.11052            0    2.7781274     13.68709    2.9115277      13990.5 

     550    -623.5004   -660.74472    37.244326    1340.1611   -1413.4326   -663.99669    41.875014    -705.8717            0    3.2519651    15.097948     2.278405      13990.5
@@ -154,21 +160,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm 
    1400   -623.50803   -660.03912     36.53109    1314.4968    362.97431   -663.24909    45.772904   -709.02199            0    3.2099708    14.566488    1.9170714      13990.5 

    1450   -623.51243   -659.65548    36.143052     1300.534    2853.0755    -663.0534    51.355353   -714.40875            0    3.3979157    15.890282    2.5251359      13990.5 

    1500   -623.51621   -661.87741    38.361201    1380.3496    740.04973   -665.00896    46.208742    -711.2177            0    3.1315492    15.168927    2.4710846      13990.5 

Loop time of 22.2766 on 1 procs for 1000 steps with 432 atoms

Loop time of 16.907 on 1 procs for 1000 steps with 432 atoms



Performance: 7.757 ns/day, 3.094 hours/ns, 44.890 timesteps/s

99.9% CPU use with 1 MPI tasks x no OpenMP threads

Performance: 10.221 ns/day, 2.348 hours/ns, 59.147 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    | 21.8       | 21.8       | 21.8       |   0.0 | 97.86

Bond    | 0.005852   | 0.005852   | 0.005852   |   0.0 |  0.03

Neigh   | 0.30423    | 0.30423    | 0.30423    |   0.0 |  1.37

Comm    | 0.14388    | 0.14388    | 0.14388    |   0.0 |  0.65

Output  | 0.0010855  | 0.0010855  | 0.0010855  |   0.0 |  0.00

Modify  | 0.0064189  | 0.0064189  | 0.0064189  |   0.0 |  0.03

Other   |            | 0.01527    |            |       |  0.07

Pair    | 16.247     | 16.247     | 16.247     |   0.0 | 96.09

Bond    | 0.0039518  | 0.0039518  | 0.0039518  |   0.0 |  0.02

Neigh   | 0.46795    | 0.46795    | 0.46795    |   0.0 |  2.77

Comm    | 0.17146    | 0.17146    | 0.17146    |   0.0 |  1.01

Output  | 0.00082397 | 0.00082397 | 0.00082397 |   0.0 |  0.00

Modify  | 0.0065799  | 0.0065799  | 0.0065799  |   0.0 |  0.04

Other   |            | 0.009467   |            |       |  0.06



Nlocal:    432 ave 432 max 432 min

Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -182,4 +188,4 @@ Ave neighs/atom = 687.803 
Ave special neighs/atom = 1

Neighbor list builds = 44

Dangerous builds = 0

Total wall time: 0:00:33
 
Total wall time: 0:00:25

examples/coreshell/log.9Nov16.coreshell.dsf.g++.4→examples/coreshell/log.27Nov18.coreshell.dsf.g++.4

+27 −25
Original line number Diff line number Diff line 
LAMMPS (26 Jan 2017)

LAMMPS (27 Nov 2018)

  using 1 OpenMP thread(s) per MPI task

# Testsystem for core-shell model compared to Mitchel and Finchham

# Hendrik Heenen, June 2014
@@ -74,7 +75,8 @@ Neighbor list info ... 
  ghost atom cutoff = 22

  binsize = 11, bins = 3 3 3

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair born/coul/dsf/cs, half, perpetual

  (1) pair born/coul/dsf/cs, perpetual

      attributes: half, newton on

      pair build: half/bin/newton

      stencil: half/bin/3d/newton

      bin: standard
@@ -88,7 +90,7 @@ fix_modify thermoberendsen temp CSequ 


timestep 0.002

run 500

Memory usage per processor = 6.8559 Mbytes

Per MPI rank memory allocation (min/avg/max) = 6.881 | 6.881 | 6.881 Mbytes

Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 

       0   -635.80596   -675.46362    39.657659         1427   -21302.622   -675.46362    1.6320365   -677.09565            0            0 1.5814015e-14 3.2317898e-15      13990.5 

      50   -634.07021   -666.11867    32.048452    1153.1982    -4560.945   -668.28236    37.756542    -706.0389            0     2.163691    13.802484     3.022372      13990.5
@@ -101,21 +103,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm 
     400   -625.09344   -661.26404      36.1706    1301.5253   -729.96729   -664.10334    43.468765   -707.57211            0    2.8392963    13.663555    1.9067551      13990.5 

     450   -624.46214   -660.01362    35.551477    1279.2474   -1617.7158   -663.06571    41.644856   -704.71057            0    3.0520921    14.527005    1.7280213      13990.5 

     500   -623.49246    -659.2527     35.76024    1286.7593   -935.99238   -662.32953    43.038808   -705.36834            0    3.0768302    14.099593    1.9831106      13990.5 

Loop time of 4.09864 on 4 procs for 500 steps with 432 atoms

Loop time of 2.44013 on 4 procs for 500 steps with 432 atoms



Performance: 21.080 ns/day, 1.139 hours/ns, 121.992 timesteps/s

99.7% CPU use with 4 MPI tasks x no OpenMP threads

Performance: 35.408 ns/day, 0.678 hours/ns, 204.907 timesteps/s

98.6% CPU use with 4 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 3.3804     | 3.568      | 3.8354     |   8.9 | 87.05

Bond    | 0.00074339 | 0.00079519 | 0.00087976 |   0.0 |  0.02

Neigh   | 0.045851   | 0.046084   | 0.046361   |   0.1 |  1.12

Comm    | 0.20413    | 0.47123    | 0.65875    |  24.3 | 11.50

Output  | 0.00044298 | 0.00046057 | 0.00051165 |   0.0 |  0.01

Modify  | 0.0064909  | 0.0067219  | 0.0069766  |   0.2 |  0.16

Other   |            | 0.005345   |            |       |  0.13

Pair    | 2.0321     | 2.1124     | 2.1759     |   3.6 | 86.57

Bond    | 0.00069523 | 0.00071579 | 0.00074148 |   0.0 |  0.03

Neigh   | 0.060491   | 0.060606   | 0.060709   |   0.0 |  2.48

Comm    | 0.19263    | 0.25562    | 0.33556    |  10.4 | 10.48

Output  | 0.00041246 | 0.00057316 | 0.0010512  |   0.0 |  0.02

Modify  | 0.0059495  | 0.0062472  | 0.006577   |   0.4 |  0.26

Other   |            | 0.00394    |            |       |  0.16



Nlocal:    108 ave 114 max 105 min

Histogram: 1 1 1 0 0 0 0 0 0 1
@@ -135,7 +137,7 @@ unfix thermoberendsen 
# ------------------------ Dynamic Run -------------------------------



run 1000

Memory usage per processor = 6.85787 Mbytes

Per MPI rank memory allocation (min/avg/max) = 6.883 | 6.948 | 7.138 Mbytes

Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 

     500   -623.49319    -659.2527    35.759511    1286.7331   -936.04802   -662.32953    43.038808   -705.36834            0    3.0768302    14.099593    1.9831106      13990.5 

     550   -623.44059   -663.57938    40.138795    1444.3127   -935.73484    -666.2789    42.563337   -708.84224            0    2.6995167    13.918509    2.3189805      13990.5
@@ -158,21 +160,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm 
    1400   -623.47124   -661.45375    37.982513    1366.7233   -379.56023    -664.6321    43.788306   -708.42041            0    3.1783497    14.251126    1.7415409      13990.5 

    1450   -623.46671   -660.17518    36.708464    1320.8792   -374.37056   -662.92706    44.083648   -707.01071            0    2.7518803    15.210167    1.9984277      13990.5 

    1500   -623.50515   -659.06488    35.559725    1279.5442    260.37822   -662.39548    45.779764   -708.17524            0    3.3306005    14.682396    2.4201107      13990.5 

Loop time of 8.26746 on 4 procs for 1000 steps with 432 atoms

Loop time of 5.16152 on 4 procs for 1000 steps with 432 atoms



Performance: 20.901 ns/day, 1.148 hours/ns, 120.956 timesteps/s

99.7% CPU use with 4 MPI tasks x no OpenMP threads

Performance: 33.478 ns/day, 0.717 hours/ns, 193.741 timesteps/s

98.3% CPU use with 4 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 6.706      | 7.1568     | 7.6597     |  12.7 | 86.57

Bond    | 0.0014617  | 0.0015531  | 0.0016506  |   0.2 |  0.02

Neigh   | 0.10511    | 0.10522    | 0.10532    |   0.0 |  1.27

Comm    | 0.48547    | 0.98841    | 1.4393     |  34.0 | 11.96

Output  | 0.0012085  | 0.0012462  | 0.0013196  |   0.1 |  0.02

Modify  | 0.0021446  | 0.0021989  | 0.0022545  |   0.1 |  0.03

Other   |            | 0.01204    |            |       |  0.15

Pair    | 4.0761     | 4.2795     | 4.6259     |  10.9 | 82.91

Bond    | 0.0013907  | 0.0014481  | 0.0015037  |   0.1 |  0.03

Neigh   | 0.13612    | 0.13618    | 0.13624    |   0.0 |  2.64

Comm    | 0.38391    | 0.73074    | 0.93346    |  26.3 | 14.16

Output  | 0.00096703 | 0.0014517  | 0.0028937  |   2.2 |  0.03

Modify  | 0.0022988  | 0.0024452  | 0.0025537  |   0.2 |  0.05

Other   |            | 0.009786   |            |       |  0.19



Nlocal:    108 ave 114 max 94 min

Histogram: 1 0 0 0 0 0 0 0 1 2
@@ -186,4 +188,4 @@ Ave neighs/atom = 687.484 
Ave special neighs/atom = 1

Neighbor list builds = 46

Dangerous builds = 0

Total wall time: 0:00:12
 
Total wall time: 0:00:07

examples/coreshell/log.27Nov18.coreshell.thermostats.g++.1

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+278 −0

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