./Stage_2/2.5_NVT.out output for 780: Na2SO4-0.5m-step 1-npt2ns-nvt2ns
Status:
finished
#-------------------------------------------------------------------------------
# Stage 2.5: NVT integration for 2 ns with a timestep of 1 fs
# Temperature 298.2 K
#-------------------------------------------------------------------------------
# Fix shake is needed for water in pcff+
fix shaken all shake .0001 20 50000 a 1 b 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
2220 = # of frozen angles
find clusters CPU = 0.001 seconds
reset_timestep 0
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
thermo ${Nthermo}
thermo 0
fix 1 movable nvt temp 298.2 298.2 100 drag 0.0
fix 2 movable ave/time 1 200000 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_averages.txt off 1
fix 3 movable ave/time 200 1 200 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_instantaneous.txt
restart 2000000 2.5.restart
dump sci all custom 200000 2.5.xyz id mol type q xs ys zs
timestep 1
run 2000000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.25520686
grid = 30 30 30
stencil order = 5
estimated absolute RMS force accuracy = 0.0027786767
estimated relative force accuracy = 8.3679023e-06
using double precision KISS FFT
3d grid and FFT values/proc = 10648 3600
generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 0
1 0.97 8.02358e-12 6660
1 103.7 6.48214e-10 2220
Per MPI rank memory allocation (min/avg/max) = 15.23 | 15.24 | 15.26 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
0 1e-06 -315.02677 67356.279 1.0560122 301.19653 31.874342 43.810725 0 0 6141.8412 84216.957 -126.69819 -124236.3 -33801.813 4111.0704
SHAKE stats (type/ave/delta/count) on step 50000
1 0.97 1.17734e-06 6660
1 103.7 9.05056e-05 2220
SHAKE stats (type/ave/delta/count) on step 100000
1 0.97 1.2677e-06 6660
1 103.7 0.000129519 2220
SHAKE stats (type/ave/delta/count) on step 150000
1 0.97 1.63949e-06 6660
1 103.7 9.59572e-05 2220
SHAKE stats (type/ave/delta/count) on step 200000
1 0.97 1.42635e-06 6660
1 103.7 0.000116894 2220
SHAKE stats (type/ave/delta/count) on step 250000
1 0.97 1.51615e-06 6660
1 103.7 9.2726e-05 2220
SHAKE stats (type/ave/delta/count) on step 300000
1 0.97 1.53609e-06 6660
1 103.7 0.000117236 2220
SHAKE stats (type/ave/delta/count) on step 350000
1 0.97 1.36573e-06 6660
1 103.7 0.000103943 2220
SHAKE stats (type/ave/delta/count) on step 400000
1 0.97 1.18888e-06 6660
1 103.7 9.39546e-05 2220
SHAKE stats (type/ave/delta/count) on step 450000
1 0.97 1.98427e-06 6660
1 103.7 0.000103841 2220
SHAKE stats (type/ave/delta/count) on step 500000
1 0.97 1.53262e-06 6660
1 103.7 0.000133769 2220
SHAKE stats (type/ave/delta/count) on step 550000
1 0.97 1.42407e-06 6660
1 103.7 9.20926e-05 2220
SHAKE stats (type/ave/delta/count) on step 600000
1 0.97 1.20572e-06 6660
1 103.7 0.000125909 2220
SHAKE stats (type/ave/delta/count) on step 650000
1 0.97 1.28063e-06 6660
1 103.7 9.52507e-05 2220
SHAKE stats (type/ave/delta/count) on step 700000
1 0.97 1.28493e-06 6660
1 103.7 9.6223e-05 2220
SHAKE stats (type/ave/delta/count) on step 750000
1 0.97 1.73035e-06 6660
1 103.7 0.000124631 2220
SHAKE stats (type/ave/delta/count) on step 800000
1 0.97 1.15463e-06 6660
1 103.7 0.00010443 2220
SHAKE stats (type/ave/delta/count) on step 850000
1 0.97 1.27296e-06 6660
1 103.7 0.000118808 2220
SHAKE stats (type/ave/delta/count) on step 900000
1 0.97 1.33813e-06 6660
1 103.7 9.6704e-05 2220
SHAKE stats (type/ave/delta/count) on step 950000
1 0.97 1.44682e-06 6660
1 103.7 0.000110657 2220
SHAKE stats (type/ave/delta/count) on step 1000000
1 0.97 1.94101e-06 6660
1 103.7 0.000112084 2220
SHAKE stats (type/ave/delta/count) on step 1050000
1 0.97 1.38481e-06 6660
1 103.7 0.000101603 2220
SHAKE stats (type/ave/delta/count) on step 1100000
1 0.97 1.8095e-06 6660
1 103.7 0.000127165 2220
SHAKE stats (type/ave/delta/count) on step 1150000
1 0.97 1.52245e-06 6660
1 103.7 0.000109784 2220
SHAKE stats (type/ave/delta/count) on step 1200000
1 0.97 1.21513e-06 6660
1 103.7 9.9105e-05 2220
SHAKE stats (type/ave/delta/count) on step 1250000
1 0.97 1.20297e-06 6660
1 103.7 0.000101891 2220
SHAKE stats (type/ave/delta/count) on step 1300000
1 0.97 1.20646e-06 6660
1 103.7 9.88174e-05 2220
SHAKE stats (type/ave/delta/count) on step 1350000
1 0.97 1.16763e-06 6660
1 103.7 8.98511e-05 2220
SHAKE stats (type/ave/delta/count) on step 1400000
1 0.97 1.20912e-06 6660
1 103.7 0.000103659 2220
SHAKE stats (type/ave/delta/count) on step 1450000
1 0.97 1.50622e-06 6660
1 103.7 0.000123406 2220
SHAKE stats (type/ave/delta/count) on step 1500000
1 0.97 1.24686e-06 6660
1 103.7 0.000101603 2220
SHAKE stats (type/ave/delta/count) on step 1550000
1 0.97 1.36389e-06 6660
1 103.7 9.95112e-05 2220
SHAKE stats (type/ave/delta/count) on step 1600000
1 0.97 1.13431e-06 6660
1 103.7 9.37613e-05 2220
SHAKE stats (type/ave/delta/count) on step 1650000
1 0.97 1.1434e-06 6660
1 103.7 9.2775e-05 2220
SHAKE stats (type/ave/delta/count) on step 1700000
1 0.97 1.54691e-06 6660
1 103.7 9.78074e-05 2220
SHAKE stats (type/ave/delta/count) on step 1750000
1 0.97 1.43856e-06 6660
1 103.7 9.96632e-05 2220
SHAKE stats (type/ave/delta/count) on step 1800000
1 0.97 1.18299e-06 6660
1 103.7 9.40325e-05 2220
SHAKE stats (type/ave/delta/count) on step 1850000
1 0.97 1.38668e-06 6660
1 103.7 0.000102622 2220
SHAKE stats (type/ave/delta/count) on step 1900000
1 0.97 1.66832e-06 6660
1 103.7 9.64303e-05 2220
SHAKE stats (type/ave/delta/count) on step 1950000
1 0.97 1.27256e-06 6660
1 103.7 8.83006e-05 2220
SHAKE stats (type/ave/delta/count) on step 2000000
1 0.97 1.1946e-06 6660
1 103.7 9.1815e-05 2220
2000000 2000000 249.50221 67356.279 1.0560122 302.55589 26.875842 41.285419 0 0 6382.6388 83788.688 -126.69819 -124229.55 -33990.065 4129.6244
Loop time of 49097 on 8 procs for 2000000 steps with 6800 atoms
Performance: 3.520 ns/day, 6.819 hours/ns, 40.736 timesteps/s
98.5% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 25269 | 28756 | 40346 |2719.9 | 58.57
Bond | 8.0391 | 9.8096 | 12.377 | 50.3 | 0.02
Kspace | 5137 | 16741 | 20235 |3569.7 | 34.10
Neigh | 2178.3 | 2181.9 | 2184.1 | 4.7 | 4.44
Comm | 487.98 | 502.38 | 525.05 | 53.4 | 1.02
Output | 0.020957 | 0.022031 | 0.022941 | 0.5 | 0.00
Modify | 838.38 | 846.05 | 850.65 | 16.7 | 1.72
Other | | 59.44 | | | 0.12
Nlocal: 850 ave 881 max 818 min
Histogram: 1 0 1 1 2 0 0 1 1 1
Nghost: 10597.8 ave 10648 max 10555 min
Histogram: 2 1 1 0 0 1 1 0 0 2
Neighs: 492861 ave 516850 max 444285 min
Histogram: 1 0 0 0 1 1 1 0 2 2
Total # of neighbors = 3942890
Ave neighs/atom = 579.83676
Ave special neighs/atom = 2.0176471
Neighbor list builds = 99090
Dangerous builds = 0
undump sci
restart 0
dump sci all custom 2000000 2.5.xyz id mol type q xs ys zs
run 0
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.25520686
grid = 30 30 30
stencil order = 5
estimated absolute RMS force accuracy = 0.0027786767
estimated relative force accuracy = 8.3679023e-06
using double precision KISS FFT
3d grid and FFT values/proc = 10648 3600
generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 2000000
1 0.97 1.1946e-06 6660
1 103.7 9.1815e-05 2220
Per MPI rank memory allocation (min/avg/max) = 15.23 | 15.25 | 15.26 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
2000000 2000000 250.18441 67356.279 1.0560122 302.55589 26.875842 41.285419 0 0 6382.6388 83788.688 -126.69819 -124229.55 -33990.065 4129.6244
Loop time of 4.04825e-06 on 8 procs for 0 steps with 6800 atoms
105.0% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.048e-06 | | |100.00
Nlocal: 850 ave 881 max 818 min
Histogram: 1 0 1 1 2 0 0 1 1 1
Nghost: 10597.8 ave 10648 max 10555 min
Histogram: 2 1 1 0 0 1 1 0 0 2
Neighs: 492861 ave 516850 max 444285 min
Histogram: 1 0 0 0 1 1 1 0 2 2
Total # of neighbors = 3942890
Ave neighs/atom = 579.83676
Ave special neighs/atom = 2.0176471
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix shaken
Total wall time: 25:31:13