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update log files for coreshell examples

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This commit is contained in:
Axel Kohlmeyer
2018-11-28 15:56:58 -05:00
parent 296cab0b09
commit 98c8f22046
10 changed files with 1157 additions and 573 deletions
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58
examples/coreshell/log.9Nov16.coreshell.dsf.g++.1 → examples/coreshell/log.27Nov18.coreshell.dsf.g++.1
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@ -1,4 +1,5 @@
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 # Testsystem for core-shell model compared to Mitchel and Finchham
# Hendrik Heenen, June 2014 # 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 velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Neighbor list info ... Neighbor list info ...
1 neighbor list requests
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
master list distance cutoff = 22 master list distance cutoff = 22
ghost atom 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 velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4 fix thermoberendsen all temp/berendsen 1427 1427 0.4
@ -84,7 +90,7 @@ fix_modify thermoberendsen temp CSequ
timestep 0.002 timestep 0.002
run 500 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 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 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 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 13990.5 400 -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 13990.5 450 -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 13990.5 500 -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 Performance: 10.244 ns/day, 2.343 hours/ns, 59.285 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads 99.8% 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 | 10.478 | 10.478 | 10.478 | 0.0 | 97.78 Pair | 8.1175 | 8.1175 | 8.1175 | 0.0 | 96.25
Bond | 0.0029511 | 0.0029511 | 0.0029511 | 0.0 | 0.03 Bond | 0.0019796 | 0.0019796 | 0.0019796 | 0.0 | 0.02
Neigh | 0.14159 | 0.14159 | 0.14159 | 0.0 | 1.32 Neigh | 0.21242 | 0.21242 | 0.21242 | 0.0 | 2.52
Comm | 0.074382 | 0.074382 | 0.074382 | 0.0 | 0.69 Comm | 0.085533 | 0.085533 | 0.085533 | 0.0 | 1.01
Output | 0.00054097 | 0.00054097 | 0.00054097 | 0.0 | 0.01 Output | 0.00041103 | 0.00041103 | 0.00041103 | 0.0 | 0.00
Modify | 0.010588 | 0.010588 | 0.010588 | 0.0 | 0.10 Modify | 0.012187 | 0.012187 | 0.012187 | 0.0 | 0.14
Other | | 0.007748 | | | 0.07 Other | | 0.003863 | | | 0.05
Nlocal: 432 ave 432 max 432 min Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -131,7 +137,7 @@ unfix thermoberendsen
# ------------------------ Dynamic Run ------------------------------- # ------------------------ Dynamic Run -------------------------------
run 1000 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 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 13990.5 500 -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 13990.5 550 -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 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 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 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 Performance: 10.221 ns/day, 2.348 hours/ns, 59.147 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads 99.9% 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 | 21.8 | 21.8 | 21.8 | 0.0 | 97.86 Pair | 16.247 | 16.247 | 16.247 | 0.0 | 96.09
Bond | 0.005852 | 0.005852 | 0.005852 | 0.0 | 0.03 Bond | 0.0039518 | 0.0039518 | 0.0039518 | 0.0 | 0.02
Neigh | 0.30423 | 0.30423 | 0.30423 | 0.0 | 1.37 Neigh | 0.46795 | 0.46795 | 0.46795 | 0.0 | 2.77
Comm | 0.14388 | 0.14388 | 0.14388 | 0.0 | 0.65 Comm | 0.17146 | 0.17146 | 0.17146 | 0.0 | 1.01
Output | 0.0010855 | 0.0010855 | 0.0010855 | 0.0 | 0.00 Output | 0.00082397 | 0.00082397 | 0.00082397 | 0.0 | 0.00
Modify | 0.0064189 | 0.0064189 | 0.0064189 | 0.0 | 0.03 Modify | 0.0065799 | 0.0065799 | 0.0065799 | 0.0 | 0.04
Other | | 0.01527 | | | 0.07 Other | | 0.009467 | | | 0.06
Nlocal: 432 ave 432 max 432 min Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0 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 Ave special neighs/atom = 1
Neighbor list builds = 44 Neighbor list builds = 44
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:33 Total wall time: 0:00:25

52
examples/coreshell/log.9Nov16.coreshell.dsf.g++.4 → examples/coreshell/log.27Nov18.coreshell.dsf.g++.4
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@ -1,4 +1,5 @@
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 # Testsystem for core-shell model compared to Mitchel and Finchham
# Hendrik Heenen, June 2014 # Hendrik Heenen, June 2014
@ -74,7 +75,8 @@ Neighbor list info ...
ghost atom 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 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 pair build: half/bin/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
@ -88,7 +90,7 @@ fix_modify thermoberendsen temp CSequ
timestep 0.002 timestep 0.002
run 500 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 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 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 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 13990.5 400 -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 13990.5 450 -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 13990.5 500 -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 Performance: 35.408 ns/day, 0.678 hours/ns, 204.907 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads 98.6% 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 | 3.3804 | 3.568 | 3.8354 | 8.9 | 87.05 Pair | 2.0321 | 2.1124 | 2.1759 | 3.6 | 86.57
Bond | 0.00074339 | 0.00079519 | 0.00087976 | 0.0 | 0.02 Bond | 0.00069523 | 0.00071579 | 0.00074148 | 0.0 | 0.03
Neigh | 0.045851 | 0.046084 | 0.046361 | 0.1 | 1.12 Neigh | 0.060491 | 0.060606 | 0.060709 | 0.0 | 2.48
Comm | 0.20413 | 0.47123 | 0.65875 | 24.3 | 11.50 Comm | 0.19263 | 0.25562 | 0.33556 | 10.4 | 10.48
Output | 0.00044298 | 0.00046057 | 0.00051165 | 0.0 | 0.01 Output | 0.00041246 | 0.00057316 | 0.0010512 | 0.0 | 0.02
Modify | 0.0064909 | 0.0067219 | 0.0069766 | 0.2 | 0.16 Modify | 0.0059495 | 0.0062472 | 0.006577 | 0.4 | 0.26
Other | | 0.005345 | | | 0.13 Other | | 0.00394 | | | 0.16
Nlocal: 108 ave 114 max 105 min Nlocal: 108 ave 114 max 105 min
Histogram: 1 1 1 0 0 0 0 0 0 1 Histogram: 1 1 1 0 0 0 0 0 0 1
@ -135,7 +137,7 @@ unfix thermoberendsen
# ------------------------ Dynamic Run ------------------------------- # ------------------------ Dynamic Run -------------------------------
run 1000 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 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 13990.5 500 -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 13990.5 550 -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 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 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 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 Performance: 33.478 ns/day, 0.717 hours/ns, 193.741 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads 98.3% 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 | 6.706 | 7.1568 | 7.6597 | 12.7 | 86.57 Pair | 4.0761 | 4.2795 | 4.6259 | 10.9 | 82.91
Bond | 0.0014617 | 0.0015531 | 0.0016506 | 0.2 | 0.02 Bond | 0.0013907 | 0.0014481 | 0.0015037 | 0.1 | 0.03
Neigh | 0.10511 | 0.10522 | 0.10532 | 0.0 | 1.27 Neigh | 0.13612 | 0.13618 | 0.13624 | 0.0 | 2.64
Comm | 0.48547 | 0.98841 | 1.4393 | 34.0 | 11.96 Comm | 0.38391 | 0.73074 | 0.93346 | 26.3 | 14.16
Output | 0.0012085 | 0.0012462 | 0.0013196 | 0.1 | 0.02 Output | 0.00096703 | 0.0014517 | 0.0028937 | 2.2 | 0.03
Modify | 0.0021446 | 0.0021989 | 0.0022545 | 0.1 | 0.03 Modify | 0.0022988 | 0.0024452 | 0.0025537 | 0.2 | 0.05
Other | | 0.01204 | | | 0.15 Other | | 0.009786 | | | 0.19
Nlocal: 108 ave 114 max 94 min Nlocal: 108 ave 114 max 94 min
Histogram: 1 0 0 0 0 0 0 0 1 2 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 Ave special neighs/atom = 1
Neighbor list builds = 46 Neighbor list builds = 46
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:12 Total wall time: 0:00:07

218
examples/coreshell/log.27Nov18.coreshell.g++.1 Normal file
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@ -0,0 +1,218 @@
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
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 1 by 1 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CStemp all temp/cs cores shells
compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CStemp press thermo_press_lmp
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Neighbor list info ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair born/coul/long/cs, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
velocity all scale 1427 temp CStemp
# thermostating using the core/shell decoupling
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CStemp
# 2 fmsec timestep
timestep 0.002
run 500
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.7895988e-14 3.594347e-15 13990.5
50 -634.17327 -666.17818 32.004909 1151.6314 -4029.8418 -667.9562 37.809071 989.23283 -1694.9981 1.7780231 9.7133792 2.191797 13990.5
100 -631.93507 -661.91226 29.977186 1078.6679 -3171.7799 -664.06719 39.33341 991.36934 -1694.7699 2.1549313 11.091423 2.1704389 13990.5
150 -630.16811 -663.12417 32.956056 1185.8565 143.26508 -665.48036 46.253769 982.97454 -1694.7087 2.3561935 11.467913 2.1652595 13990.5
200 -628.62323 -663.64922 35.025998 1260.3391 -1622.4126 -665.96878 41.661879 986.81675 -1694.4474 2.3195587 10.597709 2.9538262 13990.5
250 -627.31045 -662.01825 34.7078 1248.8894 -1509.6621 -664.50312 42.101718 987.90197 -1694.5068 2.4848739 10.392757 1.6933711 13990.5
300 -626.57622 -660.97494 34.39872 1237.7678 -1637.8094 -663.48087 41.653234 989.53228 -1694.6664 2.5059303 11.204361 2.2809738 13990.5
350 -625.91962 -665.35837 39.438749 1419.123 -1351.4779 -667.6167 41.582456 985.53382 -1694.733 2.2583289 10.83106 1.8963347 13990.5
400 -625.24849 -660.77642 35.527934 1278.4003 -424.45104 -663.12602 43.890331 987.75201 -1694.7684 2.3495966 11.521966 2.175931 13990.5
450 -624.67743 -662.88678 38.209353 1374.8857 1109.0155 -665.43212 46.964803 982.35208 -1694.749 2.5453383 11.002405 2.0014356 13990.5
500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5
Loop time of 6.53907 on 1 procs for 500 steps with 432 atoms
Performance: 13.213 ns/day, 1.816 hours/ns, 76.463 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.6198 | 5.6198 | 5.6198 | 0.0 | 85.94
Bond | 0.0020258 | 0.0020258 | 0.0020258 | 0.0 | 0.03
Kspace | 0.57813 | 0.57813 | 0.57813 | 0.0 | 8.84
Neigh | 0.23532 | 0.23532 | 0.23532 | 0.0 | 3.60
Comm | 0.086898 | 0.086898 | 0.086898 | 0.0 | 1.33
Output | 0.00044823 | 0.00044823 | 0.00044823 | 0.0 | 0.01
Modify | 0.012434 | 0.012434 | 0.012434 | 0.0 | 0.19
Other | | 0.004004 | | | 0.06
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9338 ave 9338 max 9338 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297354 ave 297354 max 297354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297354
Ave neighs/atom = 688.319
Ave special neighs/atom = 1
Neighbor list builds = 22
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5
550 -624.30709 -662.13368 37.826594 1361.1129 327.40639 -664.76823 45.306662 984.72847 -1694.8034 2.6345475 10.879928 1.9751611 13990.5
600 -624.30993 -661.84513 37.535201 1350.6277 -983.48045 -664.36158 42.366067 987.87918 -1694.6068 2.5164439 10.210733 1.7891188 13990.5
650 -624.30501 -659.20528 34.90027 1255.8151 556.10903 -661.96404 46.567866 986.0511 -1694.583 2.7587602 13.154392 2.1649995 13990.5
700 -624.30909 -661.85126 37.54217 1350.8784 -134.38128 -664.38499 44.382232 985.80624 -1694.5735 2.5337309 10.991718 2.0394718 13990.5
750 -624.30994 -660.52853 36.218591 1303.2522 1197.4475 -663.29728 47.437035 984.08807 -1694.8224 2.7687507 11.683138 2.075797 13990.5
800 -624.30475 -659.88119 35.576433 1280.1454 358.11619 -662.81702 45.487454 986.41325 -1694.7177 2.9358301 11.519677 3.7837385 13990.5
850 -624.3061 -663.63946 39.333359 1415.3307 -33.011248 -666.10531 44.296094 984.32445 -1694.7258 2.4658499 11.039607 1.9232237 13990.5
900 -624.3004 -659.038 34.737607 1249.962 373.33796 -662.10263 45.838541 986.93651 -1694.8777 3.0646238 12.13843 2.4692874 13990.5
950 -624.30802 -663.36014 39.052124 1405.2111 290.61832 -665.78004 45.269372 983.76386 -1694.8133 2.4198995 11.723515 2.0708786 13990.5
1000 -624.30213 -659.49404 35.191918 1266.3094 -920.00206 -662.25664 42.950066 989.20183 -1694.4085 2.7625985 11.442653 1.8492839 13990.5
1050 -624.30371 -659.3839 35.080191 1262.2891 284.04674 -662.15204 45.828093 986.77381 -1694.7539 2.7681351 12.123317 1.8741591 13990.5
1100 -624.3052 -660.69507 36.389872 1309.4153 -282.65356 -663.18011 44.45192 987.28618 -1694.9182 2.4850386 11.032596 1.9763392 13990.5
1150 -624.30478 -657.75327 33.448496 1203.5759 1331.9067 -660.51356 48.445972 985.91346 -1694.873 2.7602894 13.583395 2.4702797 13990.5
1200 -624.30892 -664.76096 40.452036 1455.5841 -1970.8297 -666.85506 39.983487 988.02113 -1694.8597 2.0941031 9.5654747 1.9888352 13990.5
1250 -624.30486 -661.48101 37.176152 1337.708 1864.8469 -664.22952 48.84895 981.57501 -1694.6535 2.7485121 11.090466 1.9610957 13990.5
1300 -624.3122 -662.74179 38.429588 1382.8104 1775.1061 -665.4945 48.300257 980.84489 -1694.6396 2.7527096 11.276872 1.7562916 13990.5
1350 -624.30198 -659.95211 35.65013 1282.7973 -154.85356 -662.68735 44.54654 987.24605 -1694.4799 2.7352371 11.229424 2.4657127 13990.5
1400 -624.30362 -659.14451 34.840882 1253.6781 -159.66669 -662.01516 44.455993 988.18506 -1694.6562 2.87065 11.536771 1.6678 13990.5
1450 -624.30238 -661.91803 37.615642 1353.5222 993.97328 -664.55469 46.579213 983.57987 -1694.7138 2.6366597 11.343434 2.3751981 13990.5
1500 -624.31198 -659.70757 35.395599 1273.6385 2948.584 -662.67607 51.30697 980.45677 -1694.4398 2.9684904 11.953269 2.2096873 13990.5
Loop time of 13.2154 on 1 procs for 1000 steps with 432 atoms
Performance: 13.076 ns/day, 1.835 hours/ns, 75.669 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.363 | 11.363 | 11.363 | 0.0 | 85.98
Bond | 0.0040638 | 0.0040638 | 0.0040638 | 0.0 | 0.03
Kspace | 1.1573 | 1.1573 | 1.1573 | 0.0 | 8.76
Neigh | 0.50039 | 0.50039 | 0.50039 | 0.0 | 3.79
Comm | 0.17365 | 0.17365 | 0.17365 | 0.0 | 1.31
Output | 0.00093961 | 0.00093961 | 0.00093961 | 0.0 | 0.01
Modify | 0.0068541 | 0.0068541 | 0.0068541 | 0.0 | 0.05
Other | | 0.009295 | | | 0.07
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9380 ave 9380 max 9380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 296922 ave 296922 max 296922 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 296922
Ave neighs/atom = 687.319
Ave special neighs/atom = 1
Neighbor list builds = 47
Dangerous builds = 0
Total wall time: 0:00:19

218
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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
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 2 by 2 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CStemp all temp/cs cores shells
compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CStemp press thermo_press_lmp
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Neighbor list info ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair born/coul/long/cs, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
velocity all scale 1427 temp CStemp
# thermostating using the core/shell decoupling
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CStemp
# 2 fmsec timestep
timestep 0.002
run 500
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Per MPI rank memory allocation (min/avg/max) = 15.58 | 15.58 | 15.58 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.9851021e-14 4.2188475e-15 13990.5
50 -634.17349 -666.17817 32.004686 1151.6234 -4029.8405 -667.9562 37.809075 989.23283 -1694.9981 1.778024 9.7133822 2.1917966 13990.5
100 -631.93517 -661.91227 29.977104 1078.665 -3171.8044 -664.0672 39.333371 991.36937 -1694.7699 2.1549315 11.091441 2.1704346 13990.5
150 -630.16822 -663.12423 32.956001 1185.8545 143.24615 -665.48041 46.253736 982.97453 -1694.7087 2.3561828 11.467862 2.1651517 13990.5
200 -628.6223 -663.6493 35.026994 1260.375 -1622.4428 -665.96885 41.661825 986.81675 -1694.4474 2.3195537 10.597709 2.9538132 13990.5
250 -627.31146 -662.01843 34.706968 1248.8595 -1509.7149 -664.50329 42.10159 987.90193 -1694.5068 2.4848612 10.392642 1.693337 13990.5
300 -626.57661 -660.97479 34.398178 1237.7483 -1637.8266 -663.48071 41.653258 989.53241 -1694.6664 2.5059269 11.20455 2.2814851 13990.5
350 -625.91971 -665.3583 39.438589 1419.1172 -1351.5076 -667.61665 41.582479 985.53388 -1694.733 2.2583457 10.831559 1.8963688 13990.5
400 -625.24855 -660.7758 35.527253 1278.3758 -423.70384 -663.1256 43.89223 987.7506 -1694.7684 2.349799 11.523597 2.1775994 13990.5
450 -624.6774 -662.88749 38.210092 1374.9123 1108.7784 -665.43272 46.964156 982.35233 -1694.7492 2.5452316 11.002239 2.001871 13990.5
500 -624.30227 -661.97992 37.677648 1355.7533 -998.38049 -664.60501 42.373269 987.58935 -1694.5676 2.6250971 11.151918 2.8270144 13990.5
Loop time of 1.9801 on 4 procs for 500 steps with 432 atoms
Performance: 43.634 ns/day, 0.550 hours/ns, 252.513 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 | 1.3316 | 1.4349 | 1.5717 | 7.8 | 72.46
Bond | 0.00071955 | 0.00073642 | 0.00075316 | 0.0 | 0.04
Kspace | 0.20621 | 0.33644 | 0.43824 | 15.7 | 16.99
Neigh | 0.065812 | 0.065825 | 0.065829 | 0.0 | 3.32
Comm | 0.11763 | 0.12492 | 0.12828 | 1.2 | 6.31
Output | 0.0004766 | 0.0020956 | 0.0069461 | 6.1 | 0.11
Modify | 0.0063045 | 0.0071256 | 0.0079646 | 1.0 | 0.36
Other | | 0.008101 | | | 0.41
Nlocal: 108 ave 119 max 102 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 6516 ave 6545 max 6491 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 74337.8 ave 81248 max 69989 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 297351
Ave neighs/atom = 688.312
Ave special neighs/atom = 1
Neighbor list builds = 22
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Per MPI rank memory allocation (min/avg/max) = 15.59 | 15.65 | 15.84 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -624.30215 -661.97992 37.677763 1355.7575 -998.38049 -664.60501 42.373269 987.58935 -1694.5676 2.6250971 11.151918 2.8270144 13990.5
550 -624.307 -662.13312 37.826117 1361.0957 331.61441 -664.76755 45.316291 984.7202 -1694.804 2.6344363 10.876847 1.9725627 13990.5
600 -624.30999 -661.82604 37.516052 1349.9386 -977.02006 -664.34278 42.382897 987.88146 -1694.6071 2.5167365 10.214195 1.7874159 13990.5
650 -624.30519 -659.19917 34.89398 1255.5887 549.29026 -661.95827 46.555452 986.06834 -1694.5821 2.7590968 13.15971 2.150802 13990.5
700 -624.30925 -661.91134 37.60209 1353.0346 -173.75617 -664.45296 44.284848 985.83333 -1694.5711 2.5416162 10.971743 1.9844905 13990.5
750 -624.30957 -660.4111 36.101528 1299.0399 1224.7615 -663.20844 47.513495 984.09149 -1694.8134 2.7973427 11.760288 2.1436426 13990.5
800 -624.30443 -660.29859 35.994159 1295.1764 274.44426 -663.2484 45.216978 986.25498 -1694.7204 2.9498134 11.512509 4.0054687 13990.5
850 -624.30771 -663.64907 39.341363 1415.6187 339.0107 -666.13161 45.126833 983.39086 -1694.6493 2.4825413 11.020953 2.1719529 13990.5
900 -624.30318 -658.79061 34.487426 1240.9597 326.93573 -661.83606 45.870868 987.13858 -1694.8455 3.0454534 12.639272 1.9516031 13990.5
950 -624.30275 -663.63565 39.332892 1415.3139 -668.82258 -665.98818 43.090661 985.63359 -1694.7124 2.3525337 11.014784 2.0742438 13990.5
1000 -624.30302 -660.58037 36.27735 1305.3665 -725.43356 -663.2066 42.991534 988.36047 -1694.5586 2.6262239 10.521127 1.8763991 13990.5
1050 -624.30291 -660.75751 36.454601 1311.7445 834.87442 -663.66586 46.551242 984.37581 -1694.5929 2.908347 11.20897 2.1312758 13990.5
1100 -624.30709 -663.05705 38.749955 1394.3381 -709.57897 -665.5853 42.840927 986.33077 -1694.757 2.5282501 10.630015 2.6077838 13990.5
1150 -624.31167 -663.16861 38.856933 1398.1875 -202.93169 -665.68694 43.83137 985.37199 -1694.8903 2.5183367 10.924515 2.9847813 13990.5
1200 -624.30447 -660.45656 36.152088 1300.8592 -490.40029 -663.44614 43.512278 987.25887 -1694.2173 2.9895748 11.017505 2.1685389 13990.5
1250 -624.3046 -661.95895 37.654347 1354.9149 -1405.9374 -664.49438 41.407094 988.59571 -1694.4972 2.5354305 11.05786 2.0138426 13990.5
1300 -624.30002 -659.01152 34.711493 1249.0223 414.13124 -661.65532 45.873988 986.98863 -1694.5179 2.6438076 11.612439 2.2823703 13990.5
1350 -624.31114 -659.05277 34.741631 1250.1068 795.03396 -661.48604 46.584896 986.7784 -1694.8493 2.43327 10.382832 1.616191 13990.5
1400 -624.30512 -661.30058 36.995459 1331.2062 -1144.6328 -663.78961 41.970109 989.12976 -1694.8895 2.4890256 9.9264597 2.1371617 13990.5
1450 -624.30479 -657.8718 33.567014 1207.8406 980.42716 -660.87614 47.207833 986.87048 -1694.9545 3.004339 11.783025 2.7986076 13990.5
1500 -624.30058 -658.54923 34.248643 1232.3676 -728.22612 -661.1865 43.605107 989.73327 -1694.5249 2.6372721 11.688084 2.5466244 13990.5
Loop time of 4.08004 on 4 procs for 1000 steps with 432 atoms
Performance: 42.353 ns/day, 0.567 hours/ns, 245.096 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 | 2.7379 | 2.8952 | 3.2162 | 11.5 | 70.96
Bond | 0.0014176 | 0.0015033 | 0.0016136 | 0.2 | 0.04
Kspace | 0.47825 | 0.7808 | 0.93251 | 20.9 | 19.14
Neigh | 0.13731 | 0.13815 | 0.13904 | 0.2 | 3.39
Comm | 0.23139 | 0.25066 | 0.2586 | 2.2 | 6.14
Output | 0.0010233 | 0.0015535 | 0.0031006 | 2.3 | 0.04
Modify | 0.0025311 | 0.0026742 | 0.0028279 | 0.2 | 0.07
Other | | 0.00951 | | | 0.23
Nlocal: 108 ave 116 max 98 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 6461.75 ave 6504 max 6437 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Neighs: 74412.8 ave 81159 max 68634 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 297651
Ave neighs/atom = 689.007
Ave special neighs/atom = 1
Neighbor list builds = 46
Dangerous builds = 0
Total wall time: 0:00:06

278
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Testsystem for core-shell model compared to Mitchell and Fincham
# Hendrik Heenen, June 2014
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 1 by 1 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CStemp all temp/cs cores shells
compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CStemp press thermo_press_lmp
# 2 fmsec timestep
timestep 0.002
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Neighbor list info ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair born/coul/long/cs, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
velocity all scale 1427 temp CStemp
# thermostating using the core/shell decoupling
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CStemp
run 500
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.7895988e-14 3.594347e-15 13990.5
50 -634.17327 -666.17818 32.004909 1151.6314 -4029.8418 -667.9562 37.809071 989.23283 -1694.9981 1.7780231 9.7133792 2.191797 13990.5
100 -631.93507 -661.91226 29.977186 1078.6679 -3171.7799 -664.06719 39.33341 991.36934 -1694.7699 2.1549313 11.091423 2.1704389 13990.5
150 -630.16811 -663.12417 32.956056 1185.8565 143.26508 -665.48036 46.253769 982.97454 -1694.7087 2.3561935 11.467913 2.1652595 13990.5
200 -628.62323 -663.64922 35.025998 1260.3391 -1622.4126 -665.96878 41.661879 986.81675 -1694.4474 2.3195587 10.597709 2.9538262 13990.5
250 -627.31045 -662.01825 34.7078 1248.8894 -1509.6621 -664.50312 42.101718 987.90197 -1694.5068 2.4848739 10.392757 1.6933711 13990.5
300 -626.57622 -660.97494 34.39872 1237.7678 -1637.8094 -663.48087 41.653234 989.53228 -1694.6664 2.5059303 11.204361 2.2809738 13990.5
350 -625.91962 -665.35837 39.438749 1419.123 -1351.4779 -667.6167 41.582456 985.53382 -1694.733 2.2583289 10.83106 1.8963347 13990.5
400 -625.24849 -660.77642 35.527934 1278.4003 -424.45104 -663.12602 43.890331 987.75201 -1694.7684 2.3495966 11.521966 2.175931 13990.5
450 -624.67743 -662.88678 38.209353 1374.8857 1109.0155 -665.43212 46.964803 982.35208 -1694.749 2.5453383 11.002405 2.0014356 13990.5
500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5
Loop time of 6.42035 on 1 procs for 500 steps with 432 atoms
Performance: 13.457 ns/day, 1.783 hours/ns, 77.877 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 | 5.5082 | 5.5082 | 5.5082 | 0.0 | 85.79
Bond | 0.0019779 | 0.0019779 | 0.0019779 | 0.0 | 0.03
Kspace | 0.57472 | 0.57472 | 0.57472 | 0.0 | 8.95
Neigh | 0.23256 | 0.23256 | 0.23256 | 0.0 | 3.62
Comm | 0.086275 | 0.086275 | 0.086275 | 0.0 | 1.34
Output | 0.00044322 | 0.00044322 | 0.00044322 | 0.0 | 0.01
Modify | 0.012263 | 0.012263 | 0.012263 | 0.0 | 0.19
Other | | 0.003893 | | | 0.06
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9338 ave 9338 max 9338 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297354 ave 297354 max 297354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297354
Ave neighs/atom = 688.319
Ave special neighs/atom = 1
Neighbor list builds = 22
Dangerous builds = 0
unfix thermoberendsen
unfix nve
fix npt_equ all npt temp 1427 1427 0.04 iso 0 0 0.4
fix_modify npt_equ temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar
run 500
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5
550 -615.79469 -659.53309 43.738406 1573.8374 1470.2728 -662.39233 46.796275 985.55051 -1694.7391 2.8592421 11.816222 2.0435827 13959.536
600 -620.1583 -658.0606 37.902298 1363.8369 -1976.0423 -660.62151 39.901722 994.0484 -1694.5716 2.5609098 10.333069 1.7024274 14344.949
650 -614.79177 -655.16909 40.377318 1452.8955 1369.3632 -658.06385 47.296696 989.25356 -1694.6141 2.8947623 12.7805 2.1488232 14305.838
700 -619.96986 -659.64497 39.675118 1427.6282 455.78012 -662.19977 45.29754 986.93209 -1694.4294 2.554791 10.780261 2.0068563 14432.96
750 -616.0691 -654.36205 38.29295 1377.8937 -241.86552 -657.41633 43.727007 993.62088 -1694.7642 3.0542755 11.706048 3.3689413 14829.924
800 -614.16673 -652.57617 38.409441 1382.0854 -552.93403 -655.00904 42.769389 996.79939 -1694.5778 2.4328709 11.05387 1.3686986 15324.864
850 -611.92307 -653.97912 42.056053 1513.3013 -685.21581 -656.44468 42.244804 996.03742 -1694.7269 2.4655655 11.681335 1.9879277 15467.594
900 -615.2753 -658.9358 43.660499 1571.034 -243.69139 -661.50959 43.098716 989.8049 -1694.4132 2.573788 10.674681 1.6541594 14964.747
950 -617.05845 -655.42907 38.370623 1380.6886 607.78657 -658.13583 45.497112 991.02201 -1694.6549 2.7067567 12.70332 2.4561886 14472.808
1000 -618.16527 -657.57073 39.405466 1417.9254 416.69904 -660.62844 45.155689 988.77163 -1694.5558 3.0577092 11.730529 1.8247965 14362.255
Loop time of 6.22988 on 1 procs for 500 steps with 432 atoms
Performance: 13.869 ns/day, 1.731 hours/ns, 80.258 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 | 5.2759 | 5.2759 | 5.2759 | 0.0 | 84.69
Bond | 0.0028615 | 0.0028615 | 0.0028615 | 0.0 | 0.05
Kspace | 0.57661 | 0.57661 | 0.57661 | 0.0 | 9.26
Neigh | 0.24735 | 0.24735 | 0.24735 | 0.0 | 3.97
Comm | 0.083591 | 0.083591 | 0.083591 | 0.0 | 1.34
Output | 0.0004077 | 0.0004077 | 0.0004077 | 0.0 | 0.01
Modify | 0.03937 | 0.03937 | 0.03937 | 0.0 | 0.63
Other | | 0.003794 | | | 0.06
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9025 ave 9025 max 9025 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 290026 ave 290026 max 290026 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 290026
Ave neighs/atom = 671.356
Ave special neighs/atom = 1
Neighbor list builds = 24
Dangerous builds = 0
unfix npt_equ
# ------------------------ Dynamic Run -------------------------------
fix npt_dyn all npt temp 1427 1427 0.04 iso 0 0 0.4
fix_modify npt_dyn temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar
run 1000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175163
estimated absolute RMS force accuracy = 1.51081e-05
estimated relative force accuracy = 1.0492e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
1000 -618.16527 -657.57073 39.405466 1417.9254 428.20902 -660.62844 45.155689 987.86858 -1693.6527 3.0577092 11.730529 1.8247964 14362.255
1050 -624.47216 -659.74932 35.277161 1269.3767 1023.4005 -662.65642 47.132969 983.86865 -1693.658 2.9071018 11.128238 2.4855361 14240.043
1100 -617.14258 -658.07887 40.936282 1473.0087 -664.49152 -660.92582 42.224469 990.57675 -1693.727 2.8469569 11.75658 2.4149634 14408.926
1150 -619.61978 -657.61169 37.991909 1367.0614 -465.46433 -660.31084 43.105221 989.99318 -1693.4092 2.699159 10.782062 2.1690057 14554.158
1200 -615.99237 -657.2408 41.248432 1484.2407 -813.35983 -660.07564 41.678196 991.8399 -1693.5937 2.8348373 10.545446 2.1121233 14555.425
1250 -626.68392 -658.41883 31.734906 1141.9159 -539.79478 -660.84299 44.20365 988.80199 -1693.8486 2.4241661 11.395962 2.135851 14575.926
1300 -617.50678 -657.21802 39.711239 1428.928 1685.6002 -659.90723 48.138182 985.72575 -1693.7712 2.6892077 12.721388 1.8776177 14369.009
1350 -622.21239 -658.79581 36.583414 1316.3796 -799.75314 -661.51494 42.733724 989.2771 -1693.5258 2.7191347 11.211319 2.3809801 14613.392
1400 -614.34638 -654.89562 40.549232 1459.0815 1192.2924 -657.82292 46.886633 988.93592 -1693.6455 2.927306 11.818277 2.0357932 15050.984
1450 -614.74459 -651.08463 36.340044 1307.6224 -941.42354 -653.80733 42.373988 997.48406 -1693.6654 2.7226961 11.57117 1.9107106 15667.952
1500 -608.59499 -648.39988 39.804894 1432.2979 -1036.978 -651.42193 41.284322 1000.5742 -1693.2804 3.0220531 10.965804 1.9225015 15657.799
1550 -616.75971 -653.701 36.941282 1329.2567 956.80287 -656.37213 46.958724 990.63147 -1693.9623 2.6711387 11.270035 2.1646421 15283.769
1600 -614.00249 -655.22129 41.218796 1483.1743 162.86851 -658.03388 44.578553 990.97117 -1693.5836 2.8125894 12.001595 2.1613558 15014.979
1650 -620.21853 -658.7696 38.551071 1387.1817 -15.994219 -661.3575 44.417732 988.12137 -1693.8966 2.5879024 11.60402 2.2188998 14421.685
1700 -621.65896 -660.14043 38.481472 1384.6773 374.01196 -662.88364 45.046442 985.61668 -1693.5468 2.7432107 11.020422 2.0354876 13843.115
1750 -626.52363 -662.7125 36.188873 1302.1828 246.87832 -665.23873 45.613954 983.17191 -1694.0246 2.5262291 12.801515 2.4291407 13584.377
1800 -620.84342 -658.64915 37.805737 1360.3624 1419.6927 -661.54346 47.476679 984.72199 -1693.7421 2.8943029 13.331926 2.1690676 13249.778
1850 -618.96345 -661.03809 42.074638 1513.9701 1692.1613 -663.74409 47.099139 982.71413 -1693.5574 2.7060076 11.521214 1.6552929 13269.978
1900 -622.60007 -658.68592 36.085857 1298.476 -1580.4079 -661.4614 41.163528 991.0778 -1693.7027 2.7754739 10.427911 1.946547 14057.045
1950 -613.97975 -656.9327 42.952955 1545.5745 -1163.9497 -659.48701 40.688202 993.61603 -1693.7912 2.5543044 10.621596 2.2183688 14489.331
2000 -613.52562 -654.78948 41.263864 1484.796 646.07695 -657.76756 45.489785 990.40525 -1693.6626 2.978081 12.135455 2.3293 14760.827
Loop time of 12.672 on 1 procs for 1000 steps with 432 atoms
Performance: 13.636 ns/day, 1.760 hours/ns, 78.914 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 | 10.73 | 10.73 | 10.73 | 0.0 | 84.67
Bond | 0.0057325 | 0.0057325 | 0.0057325 | 0.0 | 0.05
Kspace | 1.1532 | 1.1532 | 1.1532 | 0.0 | 9.10
Neigh | 0.52571 | 0.52571 | 0.52571 | 0.0 | 4.15
Comm | 0.17069 | 0.17069 | 0.17069 | 0.0 | 1.35
Output | 0.00081754 | 0.00081754 | 0.00081754 | 0.0 | 0.01
Modify | 0.078469 | 0.078469 | 0.078469 | 0.0 | 0.62
Other | | 0.007788 | | | 0.06
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8927 ave 8927 max 8927 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 281696 ave 281696 max 281696 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 281696
Ave neighs/atom = 652.074
Ave special neighs/atom = 1
Neighbor list builds = 50
Dangerous builds = 0
Total wall time: 0:00:25

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Testsystem for core-shell model compared to Mitchell and Fincham
# Hendrik Heenen, June 2014
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 2 by 2 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CStemp all temp/cs cores shells
compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CStemp press thermo_press_lmp
# 2 fmsec timestep
timestep 0.002
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Neighbor list info ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair born/coul/long/cs, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
velocity all scale 1427 temp CStemp
# thermostating using the core/shell decoupling
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CStemp
run 500
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Per MPI rank memory allocation (min/avg/max) = 15.58 | 15.58 | 15.58 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.9851021e-14 4.2188475e-15 13990.5
50 -634.17349 -666.17817 32.004686 1151.6234 -4029.8405 -667.9562 37.809075 989.23283 -1694.9981 1.778024 9.7133822 2.1917966 13990.5
100 -631.93517 -661.91227 29.977104 1078.665 -3171.8044 -664.0672 39.333371 991.36937 -1694.7699 2.1549315 11.091441 2.1704346 13990.5
150 -630.16822 -663.12423 32.956001 1185.8545 143.24615 -665.48041 46.253736 982.97453 -1694.7087 2.3561828 11.467862 2.1651517 13990.5
200 -628.6223 -663.6493 35.026994 1260.375 -1622.4428 -665.96885 41.661825 986.81675 -1694.4474 2.3195537 10.597709 2.9538132 13990.5
250 -627.31146 -662.01843 34.706968 1248.8595 -1509.7149 -664.50329 42.10159 987.90193 -1694.5068 2.4848612 10.392642 1.693337 13990.5
300 -626.57661 -660.97479 34.398178 1237.7483 -1637.8266 -663.48071 41.653258 989.53241 -1694.6664 2.5059269 11.20455 2.2814851 13990.5
350 -625.91971 -665.3583 39.438589 1419.1172 -1351.5076 -667.61665 41.582479 985.53388 -1694.733 2.2583457 10.831559 1.8963688 13990.5
400 -625.24855 -660.7758 35.527253 1278.3758 -423.70384 -663.1256 43.89223 987.7506 -1694.7684 2.349799 11.523597 2.1775994 13990.5
450 -624.6774 -662.88749 38.210092 1374.9123 1108.7784 -665.43272 46.964156 982.35233 -1694.7492 2.5452316 11.002239 2.001871 13990.5
500 -624.30227 -661.97992 37.677648 1355.7533 -998.38049 -664.60501 42.373269 987.58935 -1694.5676 2.6250971 11.151918 2.8270144 13990.5
Loop time of 1.9161 on 4 procs for 500 steps with 432 atoms
Performance: 45.092 ns/day, 0.532 hours/ns, 260.946 timesteps/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3101 | 1.4046 | 1.5088 | 5.9 | 73.31
Bond | 0.00073409 | 0.00074953 | 0.00076699 | 0.0 | 0.04
Kspace | 0.20996 | 0.30779 | 0.39708 | 12.0 | 16.06
Neigh | 0.065428 | 0.065516 | 0.065591 | 0.0 | 3.42
Comm | 0.12002 | 0.12628 | 0.13124 | 1.2 | 6.59
Output | 0.00047278 | 0.00062203 | 0.0010662 | 0.0 | 0.03
Modify | 0.0061893 | 0.0064721 | 0.0066924 | 0.2 | 0.34
Other | | 0.004042 | | | 0.21
Nlocal: 108 ave 119 max 102 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 6516 ave 6545 max 6491 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 74337.8 ave 81248 max 69989 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 297351
Ave neighs/atom = 688.312
Ave special neighs/atom = 1
Neighbor list builds = 22
Dangerous builds = 0
unfix thermoberendsen
unfix nve
fix npt_equ all npt temp 1427 1427 0.04 iso 0 0 0.4
fix_modify npt_equ temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar
run 500
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Per MPI rank memory allocation (min/avg/max) = 15.59 | 15.65 | 15.84 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -624.30215 -661.97992 37.677763 1355.7575 -998.38049 -664.60501 42.373269 987.58935 -1694.5676 2.6250971 11.151918 2.8270144 13990.5
550 -615.79609 -659.53283 43.736746 1573.7776 1474.8922 -662.39181 46.806896 985.54114 -1694.7399 2.858983 11.812288 2.0388938 13959.445
600 -620.14312 -658.02816 37.88504 1363.2159 -1969.137 -660.59055 39.918958 994.06227 -1694.5718 2.5623852 10.344301 1.7265857 14345.491
650 -614.8194 -655.14772 40.328319 1451.1323 1362.2165 -658.04338 47.289196 989.28021 -1694.6128 2.8956629 12.77476 2.1533941 14308.181
700 -620.02982 -659.67169 39.641877 1426.4321 437.18253 -662.22416 45.260412 986.94645 -1694.431 2.5524634 10.78512 2.0136405 14434.476
750 -616.07569 -654.50017 38.424477 1382.6265 -256.57498 -657.55133 43.657506 993.54515 -1694.754 3.0511562 11.572553 3.3391993 14823.696
800 -614.14966 -652.72914 38.579477 1388.2038 -584.44437 -655.14057 42.618194 996.80921 -1694.568 2.4114337 10.916418 1.4113651 15315.148
850 -612.16455 -653.84169 41.677135 1499.6667 -441.98725 -656.42973 42.922374 995.29998 -1694.6521 2.5880353 11.829353 2.135168 15445.115
900 -615.1092 -656.96201 41.85281 1505.988 374.2354 -659.60969 44.82627 989.96538 -1694.4013 2.6476821 11.074704 1.5105804 14959.613
950 -620.11829 -657.30032 37.18203 1337.9196 237.21273 -659.92487 44.925824 990.04501 -1694.8957 2.6245445 11.636019 2.6504684 14536.194
1000 -614.74144 -660.36077 45.619322 1641.5183 890.12037 -663.18359 45.139971 986.56616 -1694.8897 2.8228194 11.867666 2.4545613 14093.503
Loop time of 1.93169 on 4 procs for 500 steps with 432 atoms
Performance: 44.728 ns/day, 0.537 hours/ns, 258.841 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.239 | 1.3639 | 1.4951 | 8.2 | 70.61
Bond | 0.0009706 | 0.0010555 | 0.0010962 | 0.2 | 0.05
Kspace | 0.22414 | 0.34623 | 0.46491 | 15.4 | 17.92
Neigh | 0.069416 | 0.069507 | 0.06959 | 0.0 | 3.60
Comm | 0.11461 | 0.12363 | 0.13004 | 1.6 | 6.40
Output | 0.00040793 | 0.0006547 | 0.001394 | 0.0 | 0.03
Modify | 0.022097 | 0.022964 | 0.023674 | 0.4 | 1.19
Other | | 0.003751 | | | 0.19
Nlocal: 108 ave 130 max 94 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 6344.5 ave 6406 max 6272 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 72679.5 ave 88315 max 61830 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 290718
Ave neighs/atom = 672.958
Ave special neighs/atom = 1
Neighbor list builds = 24
Dangerous builds = 0
unfix npt_equ
# ------------------------ Dynamic Run -------------------------------
fix npt_dyn all npt temp 1427 1427 0.04 iso 0 0 0.4
fix_modify npt_dyn temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar
run 1000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.17523
estimated absolute RMS force accuracy = 1.49925e-05
estimated relative force accuracy = 1.04117e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Per MPI rank memory allocation (min/avg/max) = 15.59 | 15.71 | 15.84 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
1000 -614.74144 -660.36077 45.619322 1641.5183 897.55556 -663.18359 45.139971 986.31352 -1694.6371 2.8228194 11.867665 2.4545613 14093.503
1050 -618.94984 -658.03173 39.081888 1406.2821 5.4174147 -660.68647 43.84377 989.81944 -1694.3497 2.6547475 10.009866 1.6559553 14124.735
1100 -616.115 -652.50083 36.385826 1309.2698 246.27221 -655.60386 44.678646 993.96562 -1694.2481 3.1030335 12.845497 2.1365385 14269.044
1150 -612.77698 -655.40444 42.627458 1533.8622 -394.23637 -658.16511 42.232098 993.95417 -1694.3514 2.7606635 10.588799 2.0797438 14526.576
1200 -614.12785 -652.61572 38.487865 1384.9074 -1232.5709 -655.35877 40.844849 997.88225 -1694.0859 2.7430549 11.246738 2.4837618 14939.435
1250 -612.01665 -651.53067 39.514016 1421.8313 -532.88057 -654.28679 42.767165 997.1403 -1694.1943 2.7561288 12.258706 3.8726564 15369.672
1300 -616.56459 -654.91454 38.349957 1379.945 -41.331568 -657.57515 44.211159 992.57496 -1694.3613 2.6606091 11.147615 2.3545887 15492.237
1350 -609.61162 -652.77366 43.162036 1553.0979 672.33089 -655.82423 44.690532 993.39227 -1693.907 3.0505702 11.680426 1.9918324 15294.141
1400 -616.08355 -652.13969 36.056138 1297.4066 -1202.7428 -654.77053 41.470863 998.3537 -1694.5951 2.6308398 10.12054 1.9139605 15206.436
1450 -613.53416 -655.92542 42.391264 1525.3632 -225.70273 -658.53945 42.800387 993.30095 -1694.6408 2.61403 10.475263 1.5543043 14786.088
1500 -618.90281 -658.01769 39.114877 1407.4691 1689.1895 -660.56762 47.983304 985.87237 -1694.4233 2.5499298 12.160031 2.121879 14225.24
1550 -619.95625 -660.95261 40.996357 1475.1703 162.48311 -663.63715 44.435076 986.14893 -1694.2212 2.6845396 11.400162 2.1028833 14097.469
1600 -621.01142 -658.90113 37.889708 1363.3839 -1426.7573 -661.45407 41.336331 991.32904 -1694.1194 2.5529431 10.96667 1.8785672 14124.398
1650 -616.93204 -657.21145 40.27941 1449.3725 1600.8152 -659.95623 47.433021 987.26391 -1694.6532 2.7447834 12.068379 2.0232824 13868.26
1700 -613.94971 -656.25711 42.307399 1522.3455 -17.243012 -658.67143 43.416284 992.19931 -1694.287 2.4143179 10.33501 1.9231274 14268.199
1750 -614.52671 -652.83727 38.310551 1378.5271 -1505.7623 -655.2978 40.639683 998.21477 -1694.1523 2.4605373 10.777496 1.8915025 14892.754
1800 -608.85779 -650.27052 41.412727 1490.1526 -426.82921 -653.21627 42.824093 998.13559 -1694.176 2.9457492 12.624136 2.1758155 15177.014
1850 -614.3254 -653.44307 39.117675 1407.5698 -10.449183 -656.43604 44.1397 993.33969 -1693.9154 2.992966 11.306721 2.0406266 14987.262
1900 -617.0898 -655.8162 38.726395 1393.4904 -810.27608 -658.56819 42.357417 993.51569 -1694.4413 2.751989 11.117505 1.8829772 14850.207
1950 -615.58194 -657.41631 41.834372 1505.3246 1466.9904 -660.21529 47.446402 986.51421 -1694.1759 2.7989828 12.408148 2.0449602 14609.998
2000 -617.98223 -655.26933 37.287095 1341.7001 -728.80528 -658.12982 42.660772 993.38817 -1694.1788 2.8604933 11.117049 2.0691895 14608.511
Loop time of 4.08624 on 4 procs for 1000 steps with 432 atoms
Performance: 42.288 ns/day, 0.568 hours/ns, 244.724 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 | 2.5272 | 2.7629 | 3.169 | 14.9 | 67.62
Bond | 0.001961 | 0.0021452 | 0.0023017 | 0.3 | 0.05
Kspace | 0.48303 | 0.85591 | 1.0735 | 24.7 | 20.95
Neigh | 0.14933 | 0.14943 | 0.14956 | 0.0 | 3.66
Comm | 0.22499 | 0.25699 | 0.27433 | 3.8 | 6.29
Output | 0.00085068 | 0.001357 | 0.0028689 | 2.4 | 0.03
Modify | 0.048769 | 0.049731 | 0.051893 | 0.6 | 1.22
Other | | 0.00775 | | | 0.19
Nlocal: 108 ave 118 max 100 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 6291.25 ave 6323 max 6256 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 71221.2 ave 77896 max 66643 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 284885
Ave neighs/atom = 659.456
Ave special neighs/atom = 1
Neighbor list builds = 50
Dangerous builds = 0
Total wall time: 0:00:07

107
examples/coreshell/log.22Sep17.coreshell.wolf.g++.1 → examples/coreshell/log.27Nov18.coreshell.wolf.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (22 Sep 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Testsystem for core-shell model compared to Mitchel and Finchham # Testsystem for core-shell model compared to Mitchel and Finchham
# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation. # Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.
@ -92,31 +93,31 @@ run 500
Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 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 Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.2935454e-14 3.3306691e-15 13990.5 0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.2935454e-14 3.3306691e-15 13990.5
50 -635.62711 -667.67134 32.044236 1153.0465 -4533.0717 -669.45724 37.76997 -707.22721 0 1.7858939 9.6844521 2.2001656 13990.5 50 -635.62711 -667.67134 32.044236 1153.0465 -4533.0717 -669.45724 37.76997 -707.22721 0 1.7858938 9.684452 2.2001656 13990.5
100 -632.76337 -662.83035 30.066977 1081.8989 -3492.8736 -664.98454 39.197093 -704.18164 0 2.1541967 11.063962 2.1543406 13990.5 100 -632.76337 -662.83035 30.066977 1081.8989 -3492.8736 -664.98454 39.197093 -704.18164 0 2.1541967 11.063962 2.1543406 13990.5
150 -630.82538 -663.70056 32.875182 1182.9464 -74.330324 -666.12202 46.263665 -712.38569 0 2.4214607 11.739683 2.7558416 13990.5 150 -630.82538 -663.70056 32.875182 1182.9464 -74.33032 -666.12202 46.263665 -712.38569 0 2.4214607 11.739683 2.7558416 13990.5
200 -629.1541 -664.54637 35.39227 1273.5187 -1707.5508 -666.87772 41.796197 -708.67391 0 2.3313445 10.594804 3.0025376 13990.5 200 -629.1541 -664.54637 35.39227 1273.5187 -1707.5508 -666.87772 41.796197 -708.67391 0 2.3313445 10.594804 3.0025376 13990.5
250 -627.86587 -662.60879 34.742918 1250.1531 -1258.7537 -665.21416 43.017024 -708.23118 0 2.6053655 10.576999 1.8400986 13990.5 250 -627.86587 -662.60879 34.742918 1250.1531 -1258.7537 -665.21416 43.017024 -708.23118 0 2.6053655 10.576999 1.8400987 13990.5
300 -627.10755 -664.12897 37.021419 1332.1403 -1891.3466 -666.39618 40.769593 -707.16577 0 2.2672094 9.412943 1.2434258 13990.5 300 -627.10755 -664.12897 37.021419 1332.1403 -1891.3466 -666.39618 40.769593 -707.16577 0 2.2672094 9.412943 1.2434258 13990.5
350 -626.27558 -665.04303 38.767448 1394.9676 -1436.8514 -667.47081 41.854746 -709.32556 0 2.4277827 10.304721 1.977594 13990.5 350 -626.27558 -665.04303 38.767449 1394.9676 -1436.8514 -667.47081 41.854746 -709.32556 0 2.4277827 10.304721 1.977594 13990.5
400 -625.55098 -661.86388 36.312896 1306.6455 -331.92076 -664.4632 44.426542 -708.88975 0 2.599325 11.081635 2.1734468 13990.5 400 -625.55098 -661.86388 36.312896 1306.6455 -331.92076 -664.4632 44.426542 -708.88975 0 2.599325 11.081635 2.1734468 13990.5
450 -624.88626 -661.07359 36.187328 1302.1272 -2325.834 -663.6031 39.662697 -703.26579 0 2.5295037 9.9810051 1.3068929 13990.5 450 -624.88626 -661.07359 36.187328 1302.1272 -2325.834 -663.6031 39.662697 -703.26579 0 2.5295037 9.9810051 1.3068928 13990.5
500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 13990.5 500 -623.87093 -660.24145 36.370525 1308.7192 410.85327 -662.86944 45.869201 -708.73864 0 2.6279857 10.592786 1.8162328 13990.5
Loop time of 11.7065 on 1 procs for 500 steps with 432 atoms Loop time of 9.56959 on 1 procs for 500 steps with 432 atoms
Performance: 7.381 ns/day, 3.252 hours/ns, 42.711 timesteps/s Performance: 9.029 ns/day, 2.658 hours/ns, 52.249 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads 99.0% 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 | 11.535 | 11.535 | 11.535 | 0.0 | 98.54 Pair | 9.2366 | 9.2366 | 9.2366 | 0.0 | 96.52
Bond | 0.001443 | 0.001443 | 0.001443 | 0.0 | 0.01 Bond | 0.0020828 | 0.0020828 | 0.0020828 | 0.0 | 0.02
Neigh | 0.10952 | 0.10952 | 0.10952 | 0.0 | 0.94 Neigh | 0.22581 | 0.22581 | 0.22581 | 0.0 | 2.36
Comm | 0.048796 | 0.048796 | 0.048796 | 0.0 | 0.42 Comm | 0.087387 | 0.087387 | 0.087387 | 0.0 | 0.91
Output | 0.00038695 | 0.00038695 | 0.00038695 | 0.0 | 0.00 Output | 0.00043035 | 0.00043035 | 0.00043035 | 0.0 | 0.00
Modify | 0.0067511 | 0.0067511 | 0.0067511 | 0.0 | 0.06 Modify | 0.013176 | 0.013176 | 0.013176 | 0.0 | 0.14
Other | | 0.004243 | | | 0.04 Other | | 0.004087 | | | 0.04
Nlocal: 432 ave 432 max 432 min Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -138,53 +139,53 @@ unfix thermoberendsen
run 1000 run 1000
Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 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 Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 13990.5 500 -623.87093 -660.24145 36.370525 1308.7192 410.85327 -662.86944 45.869201 -708.73864 0 2.6279857 10.592786 1.8162328 13990.5
550 -623.95762 -659.99899 36.041371 1296.8752 -442.62446 -662.68699 44.004419 -706.69141 0 2.6879934 10.936057 1.7358509 13990.5 550 -623.95762 -659.99899 36.041371 1296.8752 -442.62441 -662.68699 44.004419 -706.69141 0 2.6879934 10.936057 1.7358509 13990.5
600 -624.04214 -661.21748 37.175332 1337.6785 47.615854 -663.76133 45.009742 -708.77107 0 2.5438549 11.431366 2.1185464 13990.5 600 -624.04214 -661.21748 37.175332 1337.6785 47.61587 -663.76133 45.009742 -708.77107 0 2.5438549 11.431366 2.1185465 13990.5
650 -623.98279 -661.85255 37.86976 1362.6661 -1708.3823 -664.31138 40.933446 -705.24482 0 2.4588298 9.7960191 1.4159904 13990.5 650 -623.98279 -661.85255 37.86976 1362.6661 -1708.3824 -664.31138 40.933446 -705.24482 0 2.4588297 9.7960192 1.4159906 13990.5
700 -624.02941 -661.57484 37.54543 1350.9958 -124.09512 -663.95322 44.666402 -708.61962 0 2.3783801 10.518712 2.0854584 13990.5 700 -624.02941 -661.57484 37.545431 1350.9958 -124.09619 -663.95322 44.666399 -708.61962 0 2.3783802 10.518712 2.0854583 13990.5
750 -624.03935 -661.11619 37.076837 1334.1344 -1163.2721 -663.82553 42.1219 -705.94743 0 2.7093404 10.634859 1.9381654 13990.5 750 -624.03935 -661.11619 37.076842 1334.1346 -1163.274 -663.82553 42.121895 -705.94743 0 2.70934 10.634855 1.9381646 13990.5
800 -623.98709 -659.43647 35.44938 1275.5737 -285.65702 -662.23782 44.650233 -706.88805 0 2.8013482 11.83459 3.4506407 13990.5 800 -623.98709 -659.43647 35.449379 1275.5736 -285.65541 -662.23781 44.650237 -706.88805 0 2.8013481 11.83459 3.4506393 13990.5
850 -623.96081 -661.77923 37.818422 1360.8188 -814.33212 -664.38161 42.860208 -707.24181 0 2.6023728 10.766451 2.9211132 13990.5 850 -623.96081 -661.77923 37.81842 1360.8187 -814.33165 -664.3816 42.860208 -707.24181 0 2.6023716 10.766441 2.9211138 13990.5
900 -623.96136 -662.98419 39.022831 1404.157 308.13105 -665.65877 45.053188 -710.71195 0 2.6745786 11.028799 1.8494322 13990.5 900 -623.96136 -662.9842 39.02284 1404.1573 308.1419 -665.65877 45.053211 -710.71198 0 2.674576 11.028802 1.8494293 13990.5
950 -623.91048 -660.63828 36.7278 1321.575 -445.31526 -663.79806 43.94833 -707.74639 0 3.1597729 11.852051 1.8238458 13990.5 950 -623.91049 -660.63827 36.727782 1321.5743 -445.29549 -663.79804 43.948376 -707.74641 0 3.1597692 11.852029 1.8238312 13990.5
1000 -623.90541 -661.03474 37.129332 1336.0233 522.57958 -663.50212 45.863261 -709.36538 0 2.4673781 10.949291 1.8614095 13990.5 1000 -623.90541 -661.03472 37.129304 1336.0223 522.59285 -663.50211 45.8633 -709.36541 0 2.4673901 10.949322 1.8613502 13990.5
1050 -624.01134 -660.99076 36.979422 1330.6291 -1710.2829 -663.67762 41.056102 -704.73372 0 2.6868521 10.86533 2.2154165 13990.5 1050 -624.01134 -660.99086 36.979522 1330.6327 -1710.3266 -663.6777 41.055997 -704.7337 0 2.6868396 10.865335 2.2154562 13990.5
1100 -624.02639 -660.86661 36.840225 1325.6204 1151.0236 -663.5066 47.207185 -710.71378 0 2.6399847 11.298044 1.8900703 13990.5 1100 -624.02639 -660.86653 36.840144 1325.6175 1151.2194 -663.50657 47.207655 -710.71423 0 2.6400422 11.298226 1.8901962 13990.5
1150 -624.04418 -661.29819 37.254006 1340.5094 161.09847 -663.73735 45.222561 -708.95991 0 2.4391651 11.261119 2.2245673 13990.5 1150 -624.04418 -661.29792 37.253732 1340.4996 161.18555 -663.7371 45.222823 -708.95992 0 2.4391845 11.26132 2.2249572 13990.5
1200 -624.08628 -662.39932 38.313043 1378.6168 -1405.0927 -664.93121 41.728112 -706.65933 0 2.5318927 10.458041 2.1153159 13990.5 1200 -624.08629 -662.39857 38.312276 1378.5891 -1404.3216 -664.93056 41.729944 -706.6605 0 2.5319943 10.45796 2.1150356 13990.5
1250 -624.03036 -661.25661 37.226248 1339.5106 63.407721 -663.72719 45.086961 -708.81415 0 2.4705832 11.766021 2.2297809 13990.5 1250 -624.03031 -661.25639 37.226081 1339.5046 61.673399 -663.72681 45.083327 -708.81014 0 2.4704185 11.764377 2.2300033 13990.5
1300 -623.97475 -661.55998 37.585229 1352.4278 -763.66781 -663.80645 42.870244 -706.6767 0 2.2464703 10.098322 1.7614596 13990.5 1300 -623.97477 -661.56221 37.587436 1352.5072 -766.14948 -663.8091 42.864064 -706.67316 0 2.2468911 10.098925 1.7609776 13990.5
1350 -623.93123 -660.30786 36.376631 1308.9389 -2389.8052 -663.04725 39.749029 -702.79628 0 2.7393936 10.879364 2.6622521 13990.5 1350 -623.93106 -660.2936 36.362535 1308.4317 -2387.7331 -663.03485 39.756427 -702.79127 0 2.7412491 10.88663 2.66284 13990.5
1400 -623.86468 -658.44644 34.581765 1244.3543 2262.7586 -660.95368 50.10608 -711.05976 0 2.5072434 11.528291 1.7861906 13990.5 1400 -623.86405 -658.43845 34.574407 1244.0896 2274.8627 -660.9465 50.133006 -711.0795 0 2.5080438 11.530504 1.7943496 13990.5
1450 -623.85494 -661.47216 37.617217 1353.5789 -1435.0174 -664.13587 41.701767 -705.83764 0 2.6637191 11.297444 2.0038345 13990.5 1450 -623.85491 -661.52972 37.674807 1355.6511 -1417.2183 -664.20085 41.731022 -705.93187 0 2.6711331 11.299254 1.9911762 13990.5
1500 -623.79928 -659.70124 35.901959 1291.8588 -198.39562 -662.57415 44.358482 -706.93263 0 2.872907 11.075746 2.2821286 13990.5 1500 -623.80036 -659.86071 36.060348 1297.5581 -193.90288 -662.71759 44.340486 -707.05807 0 2.8568759 11.042693 2.2234298 13990.5
Loop time of 23.4119 on 1 procs for 1000 steps with 432 atoms Loop time of 19.4477 on 1 procs for 1000 steps with 432 atoms
Performance: 7.381 ns/day, 3.252 hours/ns, 42.713 timesteps/s Performance: 8.885 ns/day, 2.701 hours/ns, 51.420 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 | 23.069 | 23.069 | 23.069 | 0.0 | 98.54 Pair | 18.754 | 18.754 | 18.754 | 0.0 | 96.43
Bond | 0.0029275 | 0.0029275 | 0.0029275 | 0.0 | 0.01 Bond | 0.0046136 | 0.0046136 | 0.0046136 | 0.0 | 0.02
Neigh | 0.22821 | 0.22821 | 0.22821 | 0.0 | 0.97 Neigh | 0.49116 | 0.49116 | 0.49116 | 0.0 | 2.53
Comm | 0.097941 | 0.097941 | 0.097941 | 0.0 | 0.42 Comm | 0.17734 | 0.17734 | 0.17734 | 0.0 | 0.91
Output | 0.00074033 | 0.00074033 | 0.00074033 | 0.0 | 0.00 Output | 0.00094318 | 0.00094318 | 0.00094318 | 0.0 | 0.00
Modify | 0.0042015 | 0.0042015 | 0.0042015 | 0.0 | 0.02 Modify | 0.007426 | 0.007426 | 0.007426 | 0.0 | 0.04
Other | | 0.00865 | | | 0.04 Other | | 0.0122 | | | 0.06
Nlocal: 432 ave 432 max 432 min Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9388 ave 9388 max 9388 min Nghost: 9382 ave 9382 max 9382 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297212 ave 297212 max 297212 min Neighs: 297191 ave 297191 max 297191 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 = 297212 Total # of neighbors = 297191
Ave neighs/atom = 687.991 Ave neighs/atom = 687.942
Ave special neighs/atom = 1 Ave special neighs/atom = 1
Neighbor list builds = 45 Neighbor list builds = 45
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:35 Total wall time: 0:00:29

103
examples/coreshell/log.22Sep17.coreshell.wolf.g++.4 → examples/coreshell/log.27Nov18.coreshell.wolf.g++.4
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@ -1,4 +1,5 @@
LAMMPS (22 Sep 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Testsystem for core-shell model compared to Mitchel and Finchham # Testsystem for core-shell model compared to Mitchel and Finchham
# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation. # Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.
@ -94,29 +95,29 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm
0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.3530839e-14 3.6429193e-15 13990.5 0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.3530839e-14 3.6429193e-15 13990.5
50 -635.62704 -667.67108 32.044047 1153.0397 -4532.6842 -669.45828 37.771018 -707.2293 0 1.787201 9.6848095 2.2028349 13990.5 50 -635.62704 -667.67108 32.044047 1153.0397 -4532.6842 -669.45828 37.771018 -707.2293 0 1.787201 9.6848095 2.2028349 13990.5
100 -632.76343 -662.83014 30.066711 1081.8893 -3493.0827 -664.98212 39.195967 -704.17809 0 2.151977 11.060773 2.1578583 13990.5 100 -632.76343 -662.83014 30.066711 1081.8893 -3493.0827 -664.98212 39.195967 -704.17809 0 2.151977 11.060773 2.1578583 13990.5
150 -630.82533 -663.70172 32.876385 1182.9897 -75.706974 -666.12608 46.261038 -712.38712 0 2.4243598 11.746728 2.7663319 13990.5 150 -630.82533 -663.70172 32.876385 1182.9897 -75.706966 -666.12608 46.261038 -712.38712 0 2.4243598 11.746728 2.7663319 13990.5
200 -629.15463 -664.55009 35.395466 1273.6337 -1707.9185 -666.88117 41.794868 -708.67604 0 2.331082 10.596229 3.0031523 13990.5 200 -629.15463 -664.55009 35.395466 1273.6337 -1707.9185 -666.88117 41.794868 -708.67604 0 2.331082 10.596229 3.0031523 13990.5
250 -627.86625 -662.60876 34.742511 1250.1384 -1263.5726 -665.214 43.005742 -708.21974 0 2.6052329 10.572641 1.841604 13990.5 250 -627.86625 -662.60876 34.742511 1250.1384 -1263.5726 -665.214 43.005742 -708.21974 0 2.6052329 10.572641 1.8416041 13990.5
300 -627.10829 -664.12159 37.013298 1331.8481 -1884.8587 -666.39136 40.786141 -707.1775 0 2.2697693 9.4160685 1.2472271 13990.5 300 -627.10829 -664.12159 37.013298 1331.8481 -1884.8587 -666.39136 40.786141 -707.1775 0 2.2697693 9.4160684 1.2472271 13990.5
350 -626.2729 -665.01858 38.745682 1394.1844 -1433.1302 -667.44315 41.864785 -709.30793 0 2.4245625 10.312641 1.9815612 13990.5 350 -626.2729 -665.01858 38.745682 1394.1844 -1433.1302 -667.44315 41.864785 -709.30793 0 2.4245625 10.312641 1.9815612 13990.5
400 -625.54274 -661.84438 36.301638 1306.2404 -355.45544 -664.4483 44.370671 -708.81897 0 2.6039276 11.076154 2.1819703 13990.5 400 -625.54274 -661.84438 36.301638 1306.2404 -355.45544 -664.4483 44.370671 -708.81897 0 2.6039277 11.076154 2.1819702 13990.5
450 -624.88802 -661.12299 36.234964 1303.8413 -2356.6101 -663.6463 39.57847 -703.22477 0 2.523314 9.8995886 1.3113549 13990.5 450 -624.88802 -661.12299 36.234964 1303.8413 -2356.6102 -663.6463 39.57847 -703.22477 0 2.523314 9.8995886 1.3113549 13990.5
500 -623.86344 -660.20235 36.338906 1307.5814 462.72862 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5 500 -623.86344 -660.20235 36.338906 1307.5814 462.72863 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5
Loop time of 4.63313 on 4 procs for 500 steps with 432 atoms Loop time of 3.06159 on 4 procs for 500 steps with 432 atoms
Performance: 18.648 ns/day, 1.287 hours/ns, 107.919 timesteps/s Performance: 28.221 ns/day, 0.850 hours/ns, 163.314 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads 95.7% 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 | 2.8133 | 3.5934 | 4.4255 | 36.3 | 77.56 Pair | 2.3967 | 2.4786 | 2.5323 | 3.3 | 80.96
Bond | 0.00042245 | 0.00050305 | 0.00059825 | 0.0 | 0.01 Bond | 0.00078011 | 0.00080734 | 0.00087595 | 0.0 | 0.03
Neigh | 0.0411 | 0.041561 | 0.04202 | 0.2 | 0.90 Neigh | 0.065675 | 0.065807 | 0.06593 | 0.0 | 2.15
Comm | 0.15622 | 0.9884 | 1.7686 | 69.2 | 21.33 Comm | 0.43311 | 0.49538 | 0.58587 | 8.0 | 16.18
Output | 0.00028311 | 0.00031345 | 0.00040011 | 0.0 | 0.01 Output | 0.00041747 | 0.00060827 | 0.0011797 | 0.0 | 0.02
Modify | 0.0039899 | 0.00403 | 0.0040654 | 0.0 | 0.09 Modify | 0.0073676 | 0.016077 | 0.024872 | 6.9 | 0.53
Other | | 0.004911 | | | 0.11 Other | | 0.004283 | | | 0.14
Nlocal: 108 ave 112 max 106 min Nlocal: 108 ave 112 max 106 min
Histogram: 2 0 0 1 0 0 0 0 0 1 Histogram: 2 0 0 1 0 0 0 0 0 1
@ -138,53 +139,53 @@ unfix thermoberendsen
run 1000 run 1000
Per MPI rank memory allocation (min/avg/max) = 6.884 | 7.01 | 7.138 Mbytes Per MPI rank memory allocation (min/avg/max) = 6.884 | 7.01 | 7.138 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -623.86344 -660.20235 36.338906 1307.5814 462.72862 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5 500 -623.86344 -660.20235 36.338906 1307.5814 462.72863 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5
550 -623.95339 -660.07946 36.126069 1299.9229 -362.67288 -662.8047 44.180832 -706.98553 0 2.725239 11.07199 2.0461377 13990.5 550 -623.95339 -660.07946 36.126069 1299.9229 -362.67285 -662.8047 44.180832 -706.98553 0 2.725239 11.07199 2.0461376 13990.5
600 -624.04508 -661.27298 37.227902 1339.5701 110.39823 -663.90927 45.166569 -709.07584 0 2.6362911 11.747923 2.1846828 13990.5 600 -624.04508 -661.27298 37.227902 1339.5701 110.39822 -663.90927 45.166569 -709.07584 0 2.6362911 11.747923 2.1846828 13990.5
650 -623.9608 -661.50573 37.544934 1350.9779 -1594.4701 -663.91531 41.226571 -705.14188 0 2.4095736 10.022027 1.6264014 13990.5 650 -623.9608 -661.50573 37.544934 1350.9779 -1594.4701 -663.91531 41.226571 -705.14188 0 2.4095736 10.022027 1.6264014 13990.5
700 -624.00658 -663.55636 39.549777 1423.1181 -588.9804 -665.88666 43.124023 -709.01068 0 2.3302979 9.924587 2.1027837 13990.5 700 -624.00658 -663.55636 39.549777 1423.1181 -588.98052 -665.88666 43.124023 -709.01068 0 2.3302979 9.9245872 2.1027837 13990.5
750 -623.99813 -659.97695 35.978816 1294.6243 -364.1415 -662.75959 43.973556 -706.73315 0 2.782646 11.487832 1.8799695 13990.5 750 -623.99813 -659.97694 35.978814 1294.6243 -364.14087 -662.75959 43.973558 -706.73315 0 2.782646 11.487833 1.8799696 13990.5
800 -624.01235 -661.04908 37.036728 1332.6911 -85.655852 -663.49204 44.570117 -708.06215 0 2.4429547 11.213149 1.6792926 13990.5 800 -624.01235 -661.04908 37.03673 1332.6912 -85.65751 -663.49204 44.570113 -708.06215 0 2.4429544 11.213146 1.6792935 13990.5
850 -624.02581 -659.39933 35.373519 1272.844 -1090.9179 -662.11969 42.375064 -704.49476 0 2.7203673 11.214629 2.2907474 13990.5 850 -624.02581 -659.39932 35.373517 1272.8439 -1090.9176 -662.11969 42.375065 -704.49476 0 2.7203674 11.21463 2.2907477 13990.5
900 -624.09244 -663.33386 39.241421 1412.0225 303.76207 -666.00593 45.332458 -711.33839 0 2.6720667 11.897188 2.0599033 13990.5 900 -624.09244 -663.33388 39.241435 1412.0231 303.76293 -666.00594 45.332457 -711.3384 0 2.6720661 11.89718 2.0599025 13990.5
950 -624.04544 -661.11578 37.070341 1333.9007 1637.6438 -663.61305 48.65892 -712.27197 0 2.49727 12.343774 2.429225 13990.5 950 -624.04544 -661.11578 37.070343 1333.9007 1637.6353 -663.61305 48.6589 -712.27195 0 2.4972693 12.343765 2.4292305 13990.5
1000 -623.95457 -661.51816 37.563586 1351.6491 -851.77182 -663.83594 42.813468 -706.64941 0 2.317782 10.251422 1.6922864 13990.5 1000 -623.95457 -661.51817 37.563599 1351.6495 -851.76774 -663.83595 42.813476 -706.64943 0 2.3177804 10.251415 1.6922809 13990.5
1050 -623.98731 -662.01988 38.032562 1368.5242 -2123.9075 -664.72609 39.917382 -704.64348 0 2.706218 9.600838 1.7365559 13990.5 1050 -623.98731 -662.01986 38.032541 1368.5235 -2123.915 -664.72608 39.917367 -704.64345 0 2.7062234 9.6008351 1.7364324 13990.5
1100 -623.9653 -659.32023 35.354929 1272.1751 -436.90576 -662.14454 44.057776 -706.20232 0 2.8243167 11.267546 2.6807602 13990.5 1100 -623.9653 -659.3203 35.355002 1272.1777 -436.97572 -662.14462 44.05761 -706.20223 0 2.8243234 11.267511 2.6807914 13990.5
1150 -624.02273 -665.13902 41.116293 1479.486 -128.13268 -667.4769 44.013761 -711.49066 0 2.3378768 10.406604 1.5102324 13990.5 1150 -624.02272 -665.13875 41.116028 1479.4764 -128.02349 -667.47666 44.014064 -711.49073 0 2.337912 10.406786 1.5105446 13990.5
1200 -623.97328 -663.08042 39.107135 1407.1905 -539.63284 -665.67946 43.319308 -708.99877 0 2.599042 10.632657 1.4608707 13990.5 1200 -623.97327 -663.08066 39.107391 1407.1997 -539.90459 -665.67972 43.318696 -708.99842 0 2.5990577 10.632743 1.4609102 13990.5
1250 -623.92529 -661.81902 37.893723 1363.5284 1708.0621 -664.63624 48.396874 -713.03311 0 2.8172251 11.369352 1.8836979 13990.5 1250 -623.92529 -661.81994 37.894649 1363.5617 1707.6307 -664.63708 48.39571 -713.03279 0 2.8171362 11.368475 1.8834293 13990.5
1300 -623.99283 -662.19734 38.204509 1374.7114 -820.77291 -664.34556 42.656202 -707.00176 0 2.1482151 10.186898 1.7081329 13990.5 1300 -623.99279 -662.19655 38.203765 1374.6846 -820.5362 -664.34485 42.656892 -707.00174 0 2.1482931 10.187738 1.7086422 13990.5
1350 -623.99798 -658.70752 34.709535 1248.9519 776.28486 -662.01647 46.925412 -708.94188 0 3.3089536 12.457581 2.5027978 13990.5 1350 -623.99805 -658.70847 34.710418 1248.9836 775.25351 -662.01721 46.922474 -708.93969 0 3.3087449 12.454651 2.5036539 13990.5
1400 -623.96941 -662.15959 38.190183 1374.1959 880.21756 -664.90452 46.628183 -711.5327 0 2.7449282 11.918894 3.0466188 13990.5 1400 -623.96952 -662.16086 38.191338 1374.2374 880.29949 -664.90588 46.628569 -711.53444 0 2.7450171 11.920421 3.0464811 13990.5
1450 -623.95068 -662.25435 38.303671 1378.2795 -391.56711 -664.7631 43.644066 -708.40716 0 2.5087493 10.465803 1.8744864 13990.5 1450 -623.9503 -662.26105 38.310754 1378.5344 -394.54404 -664.76894 43.635444 -708.40439 0 2.5078923 10.460115 1.8699789 13990.5
1500 -624.00637 -661.48756 37.481185 1348.684 430.69453 -664.32151 45.704366 -710.02587 0 2.8339501 11.650821 2.0752813 13990.5 1500 -624.00558 -661.4861 37.480516 1348.66 438.34419 -664.32045 45.721579 -710.04203 0 2.8343497 11.655942 2.0688262 13990.5
Loop time of 6.7003 on 4 procs for 1000 steps with 432 atoms Loop time of 6.53617 on 4 procs for 1000 steps with 432 atoms
Performance: 25.790 ns/day, 0.931 hours/ns, 149.247 timesteps/s Performance: 26.438 ns/day, 0.908 hours/ns, 152.995 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads 93.9% 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 | 5.9613 | 6.0752 | 6.2064 | 4.1 | 90.67 Pair | 4.8738 | 5.0908 | 5.4162 | 10.1 | 77.89
Bond | 0.00087095 | 0.00088993 | 0.00091671 | 0.0 | 0.01 Bond | 0.0016415 | 0.0017839 | 0.0019331 | 0.3 | 0.03
Neigh | 0.06494 | 0.064964 | 0.064987 | 0.0 | 0.97 Neigh | 0.15882 | 0.15886 | 0.15894 | 0.0 | 2.43
Comm | 0.41743 | 0.54863 | 0.6626 | 13.8 | 8.19 Comm | 0.93524 | 1.2478 | 1.4524 | 19.3 | 19.09
Output | 0.00053867 | 0.00059268 | 0.00074867 | 0.0 | 0.01 Output | 0.00097799 | 0.0018684 | 0.0036883 | 2.5 | 0.03
Modify | 0.0013288 | 0.0013592 | 0.0013841 | 0.1 | 0.02 Modify | 0.0027459 | 0.0028836 | 0.0030859 | 0.2 | 0.04
Other | | 0.008613 | | | 0.13 Other | | 0.03211 | | | 0.49
Nlocal: 108 ave 116 max 102 min Nlocal: 108 ave 116 max 102 min
Histogram: 2 0 0 0 0 0 0 1 0 1 Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 6504.5 ave 6624 max 6380 min Nghost: 6504.5 ave 6624 max 6380 min
Histogram: 1 1 0 0 0 0 0 0 1 1 Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 74267 ave 79230 max 70993 min Neighs: 74267.8 ave 79232 max 70988 min
Histogram: 2 0 0 0 0 1 0 0 0 1 Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 297068 Total # of neighbors = 297071
Ave neighs/atom = 687.657 Ave neighs/atom = 687.664
Ave special neighs/atom = 1 Ave special neighs/atom = 1
Neighbor list builds = 45 Neighbor list builds = 45
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:11 Total wall time: 0:00:09

209
examples/coreshell/log.5Oct16.coreshell.g++.1
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@ -1,209 +0,0 @@
LAMMPS (5 Oct 2016)
# Testsystem for core-shell model compared to Mitchel and Finchham
# Hendrik Heenen, June 2014
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 1 by 1 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CSequ all temp/cs cores shells
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CSequ
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
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
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ
# 2 fmsec timestep
timestep 0.002
run 500
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Memory usage per processor = 15.7472 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.7895988e-14 3.594347e-15 13990.5
50 -634.17327 -666.17818 32.004909 1151.6314 -4030.3308 -667.95621 37.809071 989.23282 -1694.9981 1.7780231 9.7133792 2.1917971 13990.5
100 -631.93508 -661.91226 29.977186 1078.6679 -3172.6296 -664.0672 39.333409 991.36934 -1694.7699 2.1549314 11.091424 2.1704389 13990.5
150 -630.1681 -663.12416 32.956057 1185.8565 142.25543 -665.48036 46.253767 982.97455 -1694.7087 2.3561935 11.467914 2.1652594 13990.5
200 -628.62323 -663.64923 35.025998 1260.3391 -1623.5465 -665.96879 41.661877 986.81675 -1694.4474 2.3195587 10.597709 2.9538263 13990.5
250 -627.31045 -662.01825 34.707801 1248.8894 -1510.5567 -664.50313 42.101716 987.90197 -1694.5068 2.4848735 10.392755 1.6933702 13990.5
300 -626.57622 -660.97494 34.398716 1237.7677 -1638.6653 -663.48087 41.653234 989.53228 -1694.6664 2.5059308 11.204363 2.2809764 13990.5
350 -625.91962 -665.35838 39.438756 1419.1232 -1352.4038 -667.6167 41.582459 985.53381 -1694.733 2.2583269 10.83105 1.8963306 13990.5
400 -625.24851 -660.77642 35.527912 1278.3995 -425.3358 -663.12602 43.890329 987.75201 -1694.7684 2.3495978 11.521967 2.1759207 13990.5
450 -624.67742 -662.88674 38.209317 1374.8844 1108.0844 -665.43207 46.964873 982.35206 -1694.749 2.5453361 11.002418 2.0014401 13990.5
500 -624.30218 -661.97851 37.676336 1355.7061 -999.37887 -664.60374 42.373166 987.59022 -1694.5671 2.6252269 11.153982 2.8270477 13990.5
Loop time of 8.64071 on 1 procs for 500 steps with 432 atoms
Performance: 9.999 ns/day, 2.400 hours/ns, 57.866 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.824 | 7.824 | 7.824 | 0.0 | 90.55
Bond | 0.0024104 | 0.0024104 | 0.0024104 | 0.0 | 0.03
Kspace | 0.53534 | 0.53534 | 0.53534 | 0.0 | 6.20
Neigh | 0.19522 | 0.19522 | 0.19522 | 0.0 | 2.26
Comm | 0.066091 | 0.066091 | 0.066091 | 0.0 | 0.76
Output | 0.0003643 | 0.0003643 | 0.0003643 | 0.0 | 0.00
Modify | 0.011435 | 0.011435 | 0.011435 | 0.0 | 0.13
Other | | 0.005869 | | | 0.07
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9338 ave 9338 max 9338 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297354 ave 297354 max 297354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297354
Ave neighs/atom = 688.319
Ave special neighs/atom = 1
Neighbor list builds = 22
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Memory usage per processor = 15.7472 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -624.30218 -661.97851 37.676336 1355.7061 -999.37887 -664.60374 42.373166 987.59022 -1694.5671 2.6252269 11.153982 2.8270477 13990.5
550 -624.30708 -662.13355 37.826467 1361.1083 326.46254 -664.76811 45.306636 984.72863 -1694.8034 2.6345547 10.879989 1.9751675 13990.5
600 -624.30994 -661.8449 37.534969 1350.6193 -984.35215 -664.36139 42.366573 987.8789 -1694.6069 2.516489 10.211098 1.7890339 13990.5
650 -624.30501 -659.20596 34.900952 1255.8396 554.8226 -661.96471 46.567453 986.05088 -1694.583 2.7587454 13.15403 2.1657286 13990.5
700 -624.30907 -661.85064 37.541572 1350.8569 -135.38668 -664.3843 44.382641 985.80654 -1694.5735 2.5336521 10.991882 2.0402026 13990.5
750 -624.30999 -660.52853 36.21854 1303.2503 1196.4145 -663.29701 47.437312 984.08773 -1694.822 2.7684838 11.681986 2.0756933 13990.5
800 -624.30488 -659.87594 35.571053 1279.9518 361.87762 -662.81183 45.49882 986.40712 -1694.7178 2.935891 11.519352 3.7801343 13990.5
850 -624.30607 -663.64735 39.341278 1415.6157 -42.214824 -666.11278 44.277011 984.33678 -1694.7266 2.4654311 11.03941 1.9211474 13990.5
900 -624.30048 -659.04455 34.744072 1250.1946 386.10592 -662.10941 45.864611 986.90301 -1694.877 3.0648637 12.126864 2.467969 13990.5
950 -624.30795 -663.3468 39.038856 1404.7337 289.90291 -665.76693 45.27444 983.7762 -1694.8176 2.420128 11.735744 2.053808 13990.5
1000 -624.303 -659.5513 35.248296 1268.3381 -896.7132 -662.30776 42.985505 989.11655 -1694.4098 2.7564586 11.38686 1.8136876 13990.5
1050 -624.30433 -659.21593 34.911606 1256.223 273.26272 -661.98578 45.834363 986.93885 -1694.759 2.7698415 12.201066 1.9804734 13990.5
1100 -624.3035 -660.37975 36.076254 1298.1305 40.2604 -662.88712 45.266447 986.77782 -1694.9314 2.5073688 11.366839 2.2452799 13990.5
1150 -624.30832 -658.16356 33.855242 1218.2119 905.45817 -660.85689 47.381273 986.61927 -1694.8574 2.6933378 13.157497 2.3062872 13990.5
1200 -624.30971 -665.57285 41.263142 1484.77 -2010.9356 -667.71783 39.858615 987.32002 -1694.8965 2.1449751 9.3563352 1.7115187 13990.5
1250 -624.3069 -662.41936 38.112468 1371.3994 223.85833 -665.01906 45.021425 984.67299 -1694.7135 2.5997021 10.137667 1.8129534 13990.5
1300 -624.3116 -661.73044 37.418835 1346.4405 524.83698 -664.46475 45.716001 983.98856 -1694.1693 2.734311 11.475107 2.5468008 13990.5
1350 -624.30917 -661.34529 37.036121 1332.6693 399.81653 -663.86813 45.373759 985.3362 -1694.5781 2.5228434 10.819603 2.2048214 13990.5
1400 -624.31545 -660.75213 36.43668 1311.0996 193.18853 -663.43944 45.172084 985.90744 -1694.519 2.6873128 10.597955 1.9090871 13990.5
1450 -624.30419 -660.88131 36.577122 1316.1532 530.40423 -663.62017 46.21726 984.89723 -1694.7347 2.7388564 12.015146 2.6454091 13990.5
1500 -624.30236 -660.40336 36.100999 1299.0209 -759.2259 -663.48374 43.382233 987.65506 -1694.521 3.0803837 12.48163 2.2113083 13990.5
Loop time of 17.2383 on 1 procs for 1000 steps with 432 atoms
Performance: 10.024 ns/day, 2.394 hours/ns, 58.011 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.619 | 15.619 | 15.619 | 0.0 | 90.61
Bond | 0.0048032 | 0.0048032 | 0.0048032 | 0.0 | 0.03
Kspace | 1.068 | 1.068 | 1.068 | 0.0 | 6.20
Neigh | 0.39623 | 0.39623 | 0.39623 | 0.0 | 2.30
Comm | 0.13052 | 0.13052 | 0.13052 | 0.0 | 0.76
Output | 0.00067472 | 0.00067472 | 0.00067472 | 0.0 | 0.00
Modify | 0.0071197 | 0.0071197 | 0.0071197 | 0.0 | 0.04
Other | | 0.01175 | | | 0.07
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9327 ave 9327 max 9327 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297525 ave 297525 max 297525 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297525
Ave neighs/atom = 688.715
Ave special neighs/atom = 1
Neighbor list builds = 45
Dangerous builds = 0
Total wall time: 0:00:25

209
examples/coreshell/log.5Oct16.coreshell.g++.4
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@ -1,209 +0,0 @@
LAMMPS (5 Oct 2016)
# Testsystem for core-shell model compared to Mitchel and Finchham
# Hendrik Heenen, June 2014
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 2 by 2 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CSequ all temp/cs cores shells
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CSequ
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
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
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ
# 2 fmsec timestep
timestep 0.002
run 500
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Memory usage per processor = 15.2111 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.9851021e-14 4.2188475e-15 13990.5
50 -634.17349 -666.17817 32.004686 1151.6234 -4030.346 -667.9562 37.809075 989.23283 -1694.9981 1.7780241 9.7133824 2.1917971 13990.5
100 -631.93518 -661.91229 29.977104 1078.665 -3172.6554 -664.06722 39.333371 991.36935 -1694.7699 2.1549316 11.09144 2.1704351 13990.5
150 -630.16821 -663.12421 32.956001 1185.8545 142.23746 -665.48039 46.253735 982.97455 -1694.7087 2.3561823 11.467862 2.1651502 13990.5
200 -628.62229 -663.64928 35.026994 1260.375 -1623.495 -665.96883 41.661825 986.81676 -1694.4474 2.3195535 10.597709 2.9538127 13990.5
250 -627.31146 -662.01843 34.706969 1248.8595 -1510.677 -664.50329 42.10159 987.90193 -1694.5068 2.4848607 10.392642 1.6933333 13990.5
300 -626.57662 -660.97479 34.398174 1237.7482 -1638.7013 -663.48072 41.653268 989.53239 -1694.6664 2.5059279 11.204558 2.2814875 13990.5
350 -625.91972 -665.3583 39.438581 1419.1169 -1352.428 -667.61665 41.5825 985.53386 -1694.733 2.2583465 10.831573 1.8963653 13990.5
400 -625.24854 -660.77581 35.527271 1278.3764 -424.57407 -663.12561 43.89225 987.75056 -1694.7684 2.3497967 11.523588 2.1775908 13990.5
450 -624.67739 -662.88749 38.210098 1374.9125 1107.8255 -665.43273 46.964166 982.35231 -1694.7492 2.5452345 11.00224 2.0018738 13990.5
500 -624.30227 -661.98003 37.677766 1355.7576 -999.27326 -664.60512 42.373091 987.58943 -1694.5676 2.6250858 11.151835 2.8270448 13990.5
Loop time of 2.40619 on 4 procs for 500 steps with 432 atoms
Performance: 35.907 ns/day, 0.668 hours/ns, 207.797 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7876 | 1.9016 | 2.0542 | 7.0 | 79.03
Bond | 0.00064754 | 0.0006901 | 0.00074625 | 0.1 | 0.03
Kspace | 0.16854 | 0.31596 | 0.42594 | 16.5 | 13.13
Neigh | 0.051607 | 0.051768 | 0.051931 | 0.1 | 2.15
Comm | 0.11933 | 0.12412 | 0.12769 | 0.9 | 5.16
Output | 0.00039911 | 0.00042087 | 0.00047565 | 0.2 | 0.02
Modify | 0.0059447 | 0.0063215 | 0.0067348 | 0.4 | 0.26
Other | | 0.005341 | | | 0.22
Nlocal: 108 ave 119 max 102 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Nghost: 6516 ave 6545 max 6491 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 74337.8 ave 81248 max 69989 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 297351
Ave neighs/atom = 688.312
Ave special neighs/atom = 1
Neighbor list builds = 22
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Memory usage per processor = 15.213 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -624.30215 -661.98003 37.677882 1355.7618 -999.26443 -664.60512 42.373091 987.58943 -1694.5676 2.6250858 11.151835 2.8270448 13990.5
550 -624.30702 -662.13315 37.826126 1361.096 330.71041 -664.76759 45.316349 984.7201 -1694.804 2.6344423 10.876902 1.9726348 13990.5
600 -624.31001 -661.82602 37.516015 1349.9373 -978.11503 -664.34272 42.382797 987.88159 -1694.6071 2.5166949 10.21416 1.787289 13990.5
650 -624.30516 -659.19843 34.893268 1255.5631 548.43865 -661.95754 46.556222 986.06829 -1694.582 2.7591048 13.16005 2.1511562 13990.5
700 -624.30926 -661.91108 37.601819 1353.0248 -175.1339 -664.4528 44.284398 985.834 -1694.5712 2.5417263 10.972065 1.9847042 13990.5
750 -624.30955 -660.4096 36.100048 1298.9866 1222.5932 -663.20741 47.511377 984.09471 -1694.8135 2.7978144 11.761903 2.1481489 13990.5
800 -624.30447 -660.30683 36.002357 1295.4714 270.6639 -663.25589 45.210122 986.25515 -1694.7212 2.9490566 11.50988 4.0037749 13990.5
850 -624.30774 -663.65149 39.343757 1415.7049 339.356 -666.13397 45.12874 983.38616 -1694.6489 2.4824719 11.01305 2.1691298 13990.5
900 -624.30311 -658.78647 34.483353 1240.8132 309.88983 -661.8322 45.836842 987.17541 -1694.8445 3.045732 12.635589 1.9594437 13990.5
950 -624.303 -663.59545 39.292454 1413.8588 -649.78872 -665.94289 43.141981 985.63193 -1694.7168 2.347436 11.012602 2.0685819 13990.5
1000 -624.3032 -660.59776 36.294555 1305.9856 -753.87453 -663.22012 42.930848 988.41708 -1694.568 2.6223608 10.526403 1.8887197 13990.5
1050 -624.3023 -660.7017 36.399405 1309.7584 790.88591 -663.6376 46.453299 984.4785 -1694.5694 2.9359001 11.210429 2.1822375 13990.5
1100 -624.30545 -662.76291 38.457457 1383.8132 -853.19698 -665.29416 42.533854 986.84955 -1694.6776 2.5312537 10.517674 2.6445601 13990.5
1150 -624.31539 -663.03811 38.722722 1393.3582 -380.13868 -665.58847 43.476852 985.81618 -1694.8815 2.5503626 10.818389 1.9559813 13990.5
1200 -624.3093 -659.85835 35.549055 1279.1603 44.140107 -662.93041 44.773497 986.67501 -1694.3789 3.0720506 11.310516 2.2601607 13990.5
1250 -624.30277 -663.46462 39.161852 1409.1594 -352.57297 -666.0144 43.477124 984.93408 -1694.4256 2.5497829 10.720231 1.8458373 13990.5
1300 -624.30329 -660.15937 35.85608 1290.2079 -348.83001 -662.73568 43.884677 988.07413 -1694.6945 2.5763161 11.369766 2.2580977 13990.5
1350 -624.30469 -662.72631 38.421619 1382.5236 1338.9038 -665.20399 47.35379 982.28307 -1694.8408 2.4776776 10.587886 1.7677665 13990.5
1400 -624.30499 -662.12513 37.820139 1360.8806 132.00801 -664.73589 44.55252 985.34275 -1694.6312 2.6107622 11.193448 2.1613441 13990.5
1450 -624.30207 -661.42856 37.126485 1335.9209 2069.8075 -664.07373 49.544418 981.20445 -1694.8226 2.6451763 13.011189 3.3987593 13990.5
1500 -624.29727 -656.99924 32.701969 1176.7137 504.56835 -660.08591 46.605885 987.7602 -1694.452 3.0866635 13.271242 3.025272 13990.5
Loop time of 4.96339 on 4 procs for 1000 steps with 432 atoms
Performance: 34.815 ns/day, 0.689 hours/ns, 201.475 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6491 | 3.8484 | 4.2642 | 12.4 | 77.54
Bond | 0.0013638 | 0.0014506 | 0.0016019 | 0.2 | 0.03
Kspace | 0.3347 | 0.73521 | 0.92903 | 27.3 | 14.81
Neigh | 0.10979 | 0.11008 | 0.11042 | 0.1 | 2.22
Comm | 0.23785 | 0.25289 | 0.2601 | 1.8 | 5.10
Output | 0.0008378 | 0.00088245 | 0.00098872 | 0.2 | 0.02
Modify | 0.0022187 | 0.0024077 | 0.0026662 | 0.3 | 0.05
Other | | 0.01206 | | | 0.24
Nlocal: 108 ave 112 max 102 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 6500.75 ave 6612 max 6392 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 74275 ave 77543 max 69706 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 297100
Ave neighs/atom = 687.731
Ave special neighs/atom = 1
Neighbor list builds = 45
Dangerous builds = 0
Total wall time: 0:00:07