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update log files for coreshell examples

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
# Hendrik Heenen, June 2014
@ -68,12 +69,17 @@ thermo_modify temp CSequ
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 22
ghost atom cutoff = 22
binsize = 11 -> bins = 3 3 3
binsize = 11, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair born/coul/dsf/cs, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
@ -84,7 +90,7 @@ fix_modify thermoberendsen temp CSequ
timestep 0.002
run 500
Memory usage per processor = 7.04355 Mbytes
Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -635.80596 -675.46362 39.657659 1427 -21302.622 -675.46362 1.6320365 -677.09565 0 0 1.3517686e-14 2.942091e-15 13990.5
50 -633.9898 -666.02679 32.03699 1152.7858 -4578.5681 -668.50431 37.800204 -706.30452 0 2.4775226 14.568073 4.3012389 13990.5
@ -97,21 +103,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm
400 -625.02586 -661.46042 36.434568 1311.0236 -868.2031 -664.40231 43.21398 -707.61629 0 2.9418875 14.945389 2.7493413 13990.5
450 -624.3278 -660.50844 36.180639 1301.8865 -2203.3944 -663.49896 40.008669 -703.50763 0 2.9905179 14.158866 1.7299899 13990.5
500 -623.56254 -661.33839 37.775849 1359.2869 -810.50736 -664.11652 42.993999 -707.11052 0 2.7781274 13.68709 2.9115277 13990.5
Loop time of 10.7162 on 1 procs for 500 steps with 432 atoms
Loop time of 8.43387 on 1 procs for 500 steps with 432 atoms
Performance: 8.063 ns/day, 2.977 hours/ns, 46.658 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 10.244 ns/day, 2.343 hours/ns, 59.285 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.478 | 10.478 | 10.478 | 0.0 | 97.78
Bond | 0.0029511 | 0.0029511 | 0.0029511 | 0.0 | 0.03
Neigh | 0.14159 | 0.14159 | 0.14159 | 0.0 | 1.32
Comm | 0.074382 | 0.074382 | 0.074382 | 0.0 | 0.69
Output | 0.00054097 | 0.00054097 | 0.00054097 | 0.0 | 0.01
Modify | 0.010588 | 0.010588 | 0.010588 | 0.0 | 0.10
Other | | 0.007748 | | | 0.07
Pair | 8.1175 | 8.1175 | 8.1175 | 0.0 | 96.25
Bond | 0.0019796 | 0.0019796 | 0.0019796 | 0.0 | 0.02
Neigh | 0.21242 | 0.21242 | 0.21242 | 0.0 | 2.52
Comm | 0.085533 | 0.085533 | 0.085533 | 0.0 | 1.01
Output | 0.00041103 | 0.00041103 | 0.00041103 | 0.0 | 0.00
Modify | 0.012187 | 0.012187 | 0.012187 | 0.0 | 0.14
Other | | 0.003863 | | | 0.05
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -131,7 +137,7 @@ unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Memory usage per processor = 7.04355 Mbytes
Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -623.56254 -661.33839 37.775849 1359.2869 -810.50736 -664.11652 42.993999 -707.11052 0 2.7781274 13.68709 2.9115277 13990.5
550 -623.5004 -660.74472 37.244326 1340.1611 -1413.4326 -663.99669 41.875014 -705.8717 0 3.2519651 15.097948 2.278405 13990.5
@ -154,21 +160,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm
1400 -623.50803 -660.03912 36.53109 1314.4968 362.97431 -663.24909 45.772904 -709.02199 0 3.2099708 14.566488 1.9170714 13990.5
1450 -623.51243 -659.65548 36.143052 1300.534 2853.0755 -663.0534 51.355353 -714.40875 0 3.3979157 15.890282 2.5251359 13990.5
1500 -623.51621 -661.87741 38.361201 1380.3496 740.04973 -665.00896 46.208742 -711.2177 0 3.1315492 15.168927 2.4710846 13990.5
Loop time of 22.2766 on 1 procs for 1000 steps with 432 atoms
Loop time of 16.907 on 1 procs for 1000 steps with 432 atoms
Performance: 7.757 ns/day, 3.094 hours/ns, 44.890 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 10.221 ns/day, 2.348 hours/ns, 59.147 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.8 | 21.8 | 21.8 | 0.0 | 97.86
Bond | 0.005852 | 0.005852 | 0.005852 | 0.0 | 0.03
Neigh | 0.30423 | 0.30423 | 0.30423 | 0.0 | 1.37
Comm | 0.14388 | 0.14388 | 0.14388 | 0.0 | 0.65
Output | 0.0010855 | 0.0010855 | 0.0010855 | 0.0 | 0.00
Modify | 0.0064189 | 0.0064189 | 0.0064189 | 0.0 | 0.03
Other | | 0.01527 | | | 0.07
Pair | 16.247 | 16.247 | 16.247 | 0.0 | 96.09
Bond | 0.0039518 | 0.0039518 | 0.0039518 | 0.0 | 0.02
Neigh | 0.46795 | 0.46795 | 0.46795 | 0.0 | 2.77
Comm | 0.17146 | 0.17146 | 0.17146 | 0.0 | 1.01
Output | 0.00082397 | 0.00082397 | 0.00082397 | 0.0 | 0.00
Modify | 0.0065799 | 0.0065799 | 0.0065799 | 0.0 | 0.04
Other | | 0.009467 | | | 0.06
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -182,4 +188,4 @@ Ave neighs/atom = 687.803
Ave special neighs/atom = 1
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:00:33
Total wall time: 0:00:25

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
# Hendrik Heenen, June 2014
@ -74,7 +75,8 @@ Neighbor list info ...
ghost atom cutoff = 22
binsize = 11, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair born/coul/dsf/cs, half, perpetual
(1) pair born/coul/dsf/cs, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
@ -88,7 +90,7 @@ fix_modify thermoberendsen temp CSequ
timestep 0.002
run 500
Memory usage per processor = 6.8559 Mbytes
Per MPI rank memory allocation (min/avg/max) = 6.881 | 6.881 | 6.881 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -635.80596 -675.46362 39.657659 1427 -21302.622 -675.46362 1.6320365 -677.09565 0 0 1.5814015e-14 3.2317898e-15 13990.5
50 -634.07021 -666.11867 32.048452 1153.1982 -4560.945 -668.28236 37.756542 -706.0389 0 2.163691 13.802484 3.022372 13990.5
@ -101,21 +103,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm
400 -625.09344 -661.26404 36.1706 1301.5253 -729.96729 -664.10334 43.468765 -707.57211 0 2.8392963 13.663555 1.9067551 13990.5
450 -624.46214 -660.01362 35.551477 1279.2474 -1617.7158 -663.06571 41.644856 -704.71057 0 3.0520921 14.527005 1.7280213 13990.5
500 -623.49246 -659.2527 35.76024 1286.7593 -935.99238 -662.32953 43.038808 -705.36834 0 3.0768302 14.099593 1.9831106 13990.5
Loop time of 4.09864 on 4 procs for 500 steps with 432 atoms
Loop time of 2.44013 on 4 procs for 500 steps with 432 atoms
Performance: 21.080 ns/day, 1.139 hours/ns, 121.992 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 35.408 ns/day, 0.678 hours/ns, 204.907 timesteps/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3804 | 3.568 | 3.8354 | 8.9 | 87.05
Bond | 0.00074339 | 0.00079519 | 0.00087976 | 0.0 | 0.02
Neigh | 0.045851 | 0.046084 | 0.046361 | 0.1 | 1.12
Comm | 0.20413 | 0.47123 | 0.65875 | 24.3 | 11.50
Output | 0.00044298 | 0.00046057 | 0.00051165 | 0.0 | 0.01
Modify | 0.0064909 | 0.0067219 | 0.0069766 | 0.2 | 0.16
Other | | 0.005345 | | | 0.13
Pair | 2.0321 | 2.1124 | 2.1759 | 3.6 | 86.57
Bond | 0.00069523 | 0.00071579 | 0.00074148 | 0.0 | 0.03
Neigh | 0.060491 | 0.060606 | 0.060709 | 0.0 | 2.48
Comm | 0.19263 | 0.25562 | 0.33556 | 10.4 | 10.48
Output | 0.00041246 | 0.00057316 | 0.0010512 | 0.0 | 0.02
Modify | 0.0059495 | 0.0062472 | 0.006577 | 0.4 | 0.26
Other | | 0.00394 | | | 0.16
Nlocal: 108 ave 114 max 105 min
Histogram: 1 1 1 0 0 0 0 0 0 1
@ -135,7 +137,7 @@ unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Memory usage per processor = 6.85787 Mbytes
Per MPI rank memory allocation (min/avg/max) = 6.883 | 6.948 | 7.138 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -623.49319 -659.2527 35.759511 1286.7331 -936.04802 -662.32953 43.038808 -705.36834 0 3.0768302 14.099593 1.9831106 13990.5
550 -623.44059 -663.57938 40.138795 1444.3127 -935.73484 -666.2789 42.563337 -708.84224 0 2.6995167 13.918509 2.3189805 13990.5
@ -158,21 +160,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm
1400 -623.47124 -661.45375 37.982513 1366.7233 -379.56023 -664.6321 43.788306 -708.42041 0 3.1783497 14.251126 1.7415409 13990.5
1450 -623.46671 -660.17518 36.708464 1320.8792 -374.37056 -662.92706 44.083648 -707.01071 0 2.7518803 15.210167 1.9984277 13990.5
1500 -623.50515 -659.06488 35.559725 1279.5442 260.37822 -662.39548 45.779764 -708.17524 0 3.3306005 14.682396 2.4201107 13990.5
Loop time of 8.26746 on 4 procs for 1000 steps with 432 atoms
Loop time of 5.16152 on 4 procs for 1000 steps with 432 atoms
Performance: 20.901 ns/day, 1.148 hours/ns, 120.956 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 33.478 ns/day, 0.717 hours/ns, 193.741 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.706 | 7.1568 | 7.6597 | 12.7 | 86.57
Bond | 0.0014617 | 0.0015531 | 0.0016506 | 0.2 | 0.02
Neigh | 0.10511 | 0.10522 | 0.10532 | 0.0 | 1.27
Comm | 0.48547 | 0.98841 | 1.4393 | 34.0 | 11.96
Output | 0.0012085 | 0.0012462 | 0.0013196 | 0.1 | 0.02
Modify | 0.0021446 | 0.0021989 | 0.0022545 | 0.1 | 0.03
Other | | 0.01204 | | | 0.15
Pair | 4.0761 | 4.2795 | 4.6259 | 10.9 | 82.91
Bond | 0.0013907 | 0.0014481 | 0.0015037 | 0.1 | 0.03
Neigh | 0.13612 | 0.13618 | 0.13624 | 0.0 | 2.64
Comm | 0.38391 | 0.73074 | 0.93346 | 26.3 | 14.16
Output | 0.00096703 | 0.0014517 | 0.0028937 | 2.2 | 0.03
Modify | 0.0022988 | 0.0024452 | 0.0025537 | 0.2 | 0.05
Other | | 0.009786 | | | 0.19
Nlocal: 108 ave 114 max 94 min
Histogram: 1 0 0 0 0 0 0 0 1 2
@ -186,4 +188,4 @@ Ave neighs/atom = 687.484
Ave special neighs/atom = 1
Neighbor list builds = 46
Dangerous builds = 0
Total wall time: 0:00:12
Total wall time: 0:00:07

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
# 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
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
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
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
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
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
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
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
Loop time of 11.7065 on 1 procs for 500 steps with 432 atoms
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 410.85327 -662.86944 45.869201 -708.73864 0 2.6279857 10.592786 1.8162328 13990.5
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
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 9.029 ns/day, 2.658 hours/ns, 52.249 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 | 11.535 | 11.535 | 11.535 | 0.0 | 98.54
Bond | 0.001443 | 0.001443 | 0.001443 | 0.0 | 0.01
Neigh | 0.10952 | 0.10952 | 0.10952 | 0.0 | 0.94
Comm | 0.048796 | 0.048796 | 0.048796 | 0.0 | 0.42
Output | 0.00038695 | 0.00038695 | 0.00038695 | 0.0 | 0.00
Modify | 0.0067511 | 0.0067511 | 0.0067511 | 0.0 | 0.06
Other | | 0.004243 | | | 0.04
Pair | 9.2366 | 9.2366 | 9.2366 | 0.0 | 96.52
Bond | 0.0020828 | 0.0020828 | 0.0020828 | 0.0 | 0.02
Neigh | 0.22581 | 0.22581 | 0.22581 | 0.0 | 2.36
Comm | 0.087387 | 0.087387 | 0.087387 | 0.0 | 0.91
Output | 0.00043035 | 0.00043035 | 0.00043035 | 0.0 | 0.00
Modify | 0.013176 | 0.013176 | 0.013176 | 0.0 | 0.14
Other | | 0.004087 | | | 0.04
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -138,53 +139,53 @@ unfix thermoberendsen
run 1000
Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Loop time of 23.4119 on 1 procs for 1000 steps with 432 atoms
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 -442.62441 -662.68699 44.004419 -706.69141 0 2.6879934 10.936057 1.7358509 13990.5
600 -624.04214 -661.21748 37.175332 1337.6785 47.61587 -663.76133 45.009742 -708.77107 0 2.5438549 11.431366 2.1185465 13990.5
650 -623.98279 -661.85255 37.86976 1362.6661 -1708.3824 -664.31138 40.933446 -705.24482 0 2.4588297 9.7960192 1.4159906 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 37.076842 1334.1346 -1163.274 -663.82553 42.121895 -705.94743 0 2.70934 10.634855 1.9381646 13990.5
800 -623.98709 -659.43647 35.449379 1275.5736 -285.65541 -662.23781 44.650237 -706.88805 0 2.8013481 11.83459 3.4506393 13990.5
850 -623.96081 -661.77923 37.81842 1360.8187 -814.33165 -664.3816 42.860208 -707.24181 0 2.6023716 10.766441 2.9211138 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 -623.91049 -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 -661.03472 37.129304 1336.0223 522.59285 -663.50211 45.8633 -709.36541 0 2.4673901 10.949322 1.8613502 13990.5
1050 -624.01134 -660.99086 36.979522 1330.6327 -1710.3266 -663.6777 41.055997 -704.7337 0 2.6868396 10.865335 2.2154562 13990.5
1100 -624.02639 -660.86653 36.840144 1325.6175 1151.2194 -663.50657 47.207655 -710.71423 0 2.6400422 11.298226 1.8901962 13990.5
1150 -624.04418 -661.29792 37.253732 1340.4996 161.18555 -663.7371 45.222823 -708.95992 0 2.4391845 11.26132 2.2249572 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 -624.03031 -661.25639 37.226081 1339.5046 61.673399 -663.72681 45.083327 -708.81014 0 2.4704185 11.764377 2.2300033 13990.5
1300 -623.97477 -661.56221 37.587436 1352.5072 -766.14948 -663.8091 42.864064 -706.67316 0 2.2468911 10.098925 1.7609776 13990.5
1350 -623.93106 -660.2936 36.362535 1308.4317 -2387.7331 -663.03485 39.756427 -702.79127 0 2.7412491 10.88663 2.66284 13990.5
1400 -623.86405 -658.43845 34.574407 1244.0896 2274.8627 -660.9465 50.133006 -711.0795 0 2.5080438 11.530504 1.7943496 13990.5
1450 -623.85491 -661.52972 37.674807 1355.6511 -1417.2183 -664.20085 41.731022 -705.93187 0 2.6711331 11.299254 1.9911762 13990.5
1500 -623.80036 -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 19.4477 on 1 procs for 1000 steps with 432 atoms
Performance: 7.381 ns/day, 3.252 hours/ns, 42.713 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 8.885 ns/day, 2.701 hours/ns, 51.420 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 23.069 | 23.069 | 23.069 | 0.0 | 98.54
Bond | 0.0029275 | 0.0029275 | 0.0029275 | 0.0 | 0.01
Neigh | 0.22821 | 0.22821 | 0.22821 | 0.0 | 0.97
Comm | 0.097941 | 0.097941 | 0.097941 | 0.0 | 0.42
Output | 0.00074033 | 0.00074033 | 0.00074033 | 0.0 | 0.00
Modify | 0.0042015 | 0.0042015 | 0.0042015 | 0.0 | 0.02
Other | | 0.00865 | | | 0.04
Pair | 18.754 | 18.754 | 18.754 | 0.0 | 96.43
Bond | 0.0046136 | 0.0046136 | 0.0046136 | 0.0 | 0.02
Neigh | 0.49116 | 0.49116 | 0.49116 | 0.0 | 2.53
Comm | 0.17734 | 0.17734 | 0.17734 | 0.0 | 0.91
Output | 0.00094318 | 0.00094318 | 0.00094318 | 0.0 | 0.00
Modify | 0.007426 | 0.007426 | 0.007426 | 0.0 | 0.04
Other | | 0.0122 | | | 0.06
Nlocal: 432 ave 432 max 432 min
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
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
Total # of neighbors = 297212
Ave neighs/atom = 687.991
Total # of neighbors = 297191
Ave neighs/atom = 687.942
Ave special neighs/atom = 1
Neighbor list builds = 45
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
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
# 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
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
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
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
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
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 9.4160684 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
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
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
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
Loop time of 4.63313 on 4 procs for 500 steps with 432 atoms
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 -2356.6102 -663.6463 39.57847 -703.22477 0 2.523314 9.8995886 1.3113549 13990.5
500 -623.86344 -660.20235 36.338906 1307.5814 462.72863 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5
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
99.4% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 28.221 ns/day, 0.850 hours/ns, 163.314 timesteps/s
95.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8133 | 3.5934 | 4.4255 | 36.3 | 77.56
Bond | 0.00042245 | 0.00050305 | 0.00059825 | 0.0 | 0.01
Neigh | 0.0411 | 0.041561 | 0.04202 | 0.2 | 0.90
Comm | 0.15622 | 0.9884 | 1.7686 | 69.2 | 21.33
Output | 0.00028311 | 0.00031345 | 0.00040011 | 0.0 | 0.01
Modify | 0.0039899 | 0.00403 | 0.0040654 | 0.0 | 0.09
Other | | 0.004911 | | | 0.11
Pair | 2.3967 | 2.4786 | 2.5323 | 3.3 | 80.96
Bond | 0.00078011 | 0.00080734 | 0.00087595 | 0.0 | 0.03
Neigh | 0.065675 | 0.065807 | 0.06593 | 0.0 | 2.15
Comm | 0.43311 | 0.49538 | 0.58587 | 8.0 | 16.18
Output | 0.00041747 | 0.00060827 | 0.0011797 | 0.0 | 0.02
Modify | 0.0073676 | 0.016077 | 0.024872 | 6.9 | 0.53
Other | | 0.004283 | | | 0.14
Nlocal: 108 ave 112 max 106 min
Histogram: 2 0 0 1 0 0 0 0 0 1
@ -138,53 +139,53 @@ unfix thermoberendsen
run 1000
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
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
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
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
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 -362.67285 -662.8047 44.180832 -706.98553 0 2.725239 11.07199 2.0461376 13990.5
600 -624.04508 -661.27298 37.227902 1339.5701 110.39822 -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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Loop time of 6.7003 on 4 procs for 1000 steps with 432 atoms
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 -659.97694 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 37.03673 1332.6912 -85.65751 -663.49204 44.570113 -708.06215 0 2.4429544 11.213146 1.6792935 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 -663.33388 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 37.070343 1333.9007 1637.6353 -663.61305 48.6589 -712.27195 0 2.4972693 12.343765 2.4292305 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 -662.01986 38.032541 1368.5235 -2123.915 -664.72608 39.917367 -704.64345 0 2.7062234 9.6008351 1.7364324 13990.5
1100 -623.9653 -659.3203 35.355002 1272.1777 -436.97572 -662.14462 44.05761 -706.20223 0 2.8243234 11.267511 2.6807914 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 -623.97327 -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 -661.81994 37.894649 1363.5617 1707.6307 -664.63708 48.39571 -713.03279 0 2.8171362 11.368475 1.8834293 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 -623.99805 -658.70847 34.710418 1248.9836 775.25351 -662.01721 46.922474 -708.93969 0 3.3087449 12.454651 2.5036539 13990.5
1400 -623.96952 -662.16086 38.191338 1374.2374 880.29949 -664.90588 46.628569 -711.53444 0 2.7450171 11.920421 3.0464811 13990.5
1450 -623.9503 -662.26105 38.310754 1378.5344 -394.54404 -664.76894 43.635444 -708.40439 0 2.5078923 10.460115 1.8699789 13990.5
1500 -624.00558 -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 6.53617 on 4 procs for 1000 steps with 432 atoms
Performance: 25.790 ns/day, 0.931 hours/ns, 149.247 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 26.438 ns/day, 0.908 hours/ns, 152.995 timesteps/s
93.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.9613 | 6.0752 | 6.2064 | 4.1 | 90.67
Bond | 0.00087095 | 0.00088993 | 0.00091671 | 0.0 | 0.01
Neigh | 0.06494 | 0.064964 | 0.064987 | 0.0 | 0.97
Comm | 0.41743 | 0.54863 | 0.6626 | 13.8 | 8.19
Output | 0.00053867 | 0.00059268 | 0.00074867 | 0.0 | 0.01
Modify | 0.0013288 | 0.0013592 | 0.0013841 | 0.1 | 0.02
Other | | 0.008613 | | | 0.13
Pair | 4.8738 | 5.0908 | 5.4162 | 10.1 | 77.89
Bond | 0.0016415 | 0.0017839 | 0.0019331 | 0.3 | 0.03
Neigh | 0.15882 | 0.15886 | 0.15894 | 0.0 | 2.43
Comm | 0.93524 | 1.2478 | 1.4524 | 19.3 | 19.09
Output | 0.00097799 | 0.0018684 | 0.0036883 | 2.5 | 0.03
Modify | 0.0027459 | 0.0028836 | 0.0030859 | 0.2 | 0.04
Other | | 0.03211 | | | 0.49
Nlocal: 108 ave 116 max 102 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 6504.5 ave 6624 max 6380 min
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
Total # of neighbors = 297068
Ave neighs/atom = 687.657
Total # of neighbors = 297071
Ave neighs/atom = 687.664
Ave special neighs/atom = 1
Neighbor list builds = 45
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