#-------------------------------------------------------------------------------
# Stage 2.4: 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 2 b 2
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
2812 = # 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 2.4_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 2.4_instantaneous.txt
restart 2000000 2.4.restart
dump sci all custom 200000 2.4.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) = 0.2557377
grid = 27 27 54
stencil order = 5
estimated absolute RMS force accuracy = 0.0032430487
estimated relative force accuracy = 9.7663448e-06
using double precision KISS FFT
3d grid and FFT values/proc = 8000 2916
generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 0
2 0.992743 0.752798 8436
2 96.6024 39.773 2812
Per MPI rank memory allocation (min/avg/max) = 13.92 | 14.03 | 14.18 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 24554.333 93962.523 1.2789064 429.73544 369.51207 354.0537 0 0 24972.134 64435.033 -220.49494 -203923.09 -113792.35 8166.1181
SHAKE stats (type/ave/delta/count) on step 50000
2 0.97 1.11361e-06 8436
2 103.7 9.36979e-05 2812
SHAKE stats (type/ave/delta/count) on step 100000
2 0.97 1.18448e-06 8436
2 103.7 0.000100736 2812
SHAKE stats (type/ave/delta/count) on step 150000
2 0.97 1.1296e-06 8436
2 103.7 0.000101381 2812
SHAKE stats (type/ave/delta/count) on step 200000
2 0.97 1.19899e-06 8436
2 103.7 9.17686e-05 2812
SHAKE stats (type/ave/delta/count) on step 250000
2 0.97 9.94734e-07 8436
2 103.7 8.69421e-05 2812
SHAKE stats (type/ave/delta/count) on step 300000
2 0.97 1.30138e-06 8436
2 103.7 9.14207e-05 2812
SHAKE stats (type/ave/delta/count) on step 350000
2 0.97 1.18948e-06 8436
2 103.7 9.82604e-05 2812
SHAKE stats (type/ave/delta/count) on step 400000
2 0.97 1.21406e-06 8436
2 103.7 0.000104096 2812
SHAKE stats (type/ave/delta/count) on step 450000
2 0.97 1.23807e-06 8436
2 103.7 9.38467e-05 2812
SHAKE stats (type/ave/delta/count) on step 500000
2 0.97 1.21409e-06 8436
2 103.7 9.28918e-05 2812
SHAKE stats (type/ave/delta/count) on step 550000
2 0.97 1.56521e-06 8436
2 103.7 0.000106609 2812
SHAKE stats (type/ave/delta/count) on step 600000
2 0.97 1.78265e-06 8436
2 103.7 0.000117609 2812
SHAKE stats (type/ave/delta/count) on step 650000
2 0.97 1.50347e-06 8436
2 103.7 9.6015e-05 2812
SHAKE stats (type/ave/delta/count) on step 700000
2 0.97 1.16298e-06 8436
2 103.7 0.000106746 2812
SHAKE stats (type/ave/delta/count) on step 750000
2 0.97 1.37701e-06 8436
2 103.7 9.74288e-05 2812
SHAKE stats (type/ave/delta/count) on step 800000
2 0.97 1.36784e-06 8436
2 103.7 0.000100405 2812
SHAKE stats (type/ave/delta/count) on step 850000
2 0.97 1.22288e-06 8436
2 103.7 9.12062e-05 2812
SHAKE stats (type/ave/delta/count) on step 900000
2 0.97 1.02429e-06 8436
2 103.7 0.000101854 2812
SHAKE stats (type/ave/delta/count) on step 950000
2 0.97 1.20741e-06 8436
2 103.7 9.1817e-05 2812
SHAKE stats (type/ave/delta/count) on step 1000000
2 0.97 1.18464e-06 8436
2 103.7 9.07524e-05 2812
SHAKE stats (type/ave/delta/count) on step 1050000
2 0.97 1.78543e-06 8436
2 103.7 0.000139137 2812
SHAKE stats (type/ave/delta/count) on step 1100000
2 0.97 1.28496e-06 8436
2 103.7 9.81142e-05 2812
SHAKE stats (type/ave/delta/count) on step 1150000
2 0.97 1.39862e-06 8436
2 103.7 0.000110183 2812
SHAKE stats (type/ave/delta/count) on step 1200000
2 0.97 1.28141e-06 8436
2 103.7 0.000104359 2812
SHAKE stats (type/ave/delta/count) on step 1250000
2 0.97 1.90778e-06 8436
2 103.7 0.000112799 2812
SHAKE stats (type/ave/delta/count) on step 1300000
2 0.97 1.5079e-06 8436
2 103.7 0.000106267 2812
SHAKE stats (type/ave/delta/count) on step 1350000
2 0.97 1.39171e-06 8436
2 103.7 0.00010803 2812
SHAKE stats (type/ave/delta/count) on step 1400000
2 0.97 1.20809e-06 8436
2 103.7 9.76712e-05 2812
SHAKE stats (type/ave/delta/count) on step 1450000
2 0.97 1.12478e-06 8436
2 103.7 9.87808e-05 2812
SHAKE stats (type/ave/delta/count) on step 1500000
2 0.97 1.2679e-06 8436
2 103.7 0.000111549 2812
SHAKE stats (type/ave/delta/count) on step 1550000
2 0.97 1.24903e-06 8436
2 103.7 9.8847e-05 2812
SHAKE stats (type/ave/delta/count) on step 1600000
2 0.97 1.44408e-06 8436
2 103.7 9.34618e-05 2812
SHAKE stats (type/ave/delta/count) on step 1650000
2 0.97 1.33934e-06 8436
2 103.7 9.96517e-05 2812
SHAKE stats (type/ave/delta/count) on step 1700000
2 0.97 1.50295e-06 8436
2 103.7 0.000108509 2812
SHAKE stats (type/ave/delta/count) on step 1750000
2 0.97 1.13434e-06 8436
2 103.7 0.000101223 2812
SHAKE stats (type/ave/delta/count) on step 1800000
2 0.97 1.57493e-06 8436
2 103.7 0.000113958 2812
SHAKE stats (type/ave/delta/count) on step 1850000
2 0.97 1.13778e-06 8436
2 103.7 9.66551e-05 2812
SHAKE stats (type/ave/delta/count) on step 1900000
2 0.97 1.29693e-06 8436
2 103.7 9.81422e-05 2812
SHAKE stats (type/ave/delta/count) on step 1950000
2 0.97 1.20657e-06 8436
2 103.7 0.000108238 2812
SHAKE stats (type/ave/delta/count) on step 2000000
2 0.97 1.40185e-06 8436
2 103.7 0.000106286 2812
2000000 2000000 2128.49 93962.523 1.2789064 296.95398 52.106796 83.455533 0 0 19559.57 46218.761 -220.49494 -206915.39 -141001.49 5642.9167
Loop time of 22638.8 on 16 procs for 2000000 steps with 9188 atoms
Performance: 7.633 ns/day, 3.144 hours/ns, 88.344 timesteps/s
99.3% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15178 | 15780 | 16389 | 310.5 | 69.70
Bond | 5.2654 | 7.8801 | 11.726 | 63.0 | 0.03
Kspace | 3758.4 | 4360.3 | 4958.2 | 582.8 | 19.26
Neigh | 911.92 | 912.51 | 913.15 | 1.5 | 4.03
Comm | 697.08 | 707.31 | 716.7 | 25.6 | 3.12
Output | 0.013541 | 0.015406 | 0.017172 | 0.9 | 0.00
Modify | 818.81 | 822.7 | 828.32 | 8.7 | 3.63
Other | | 48.38 | | | 0.21
Nlocal: 574.25 ave 588 max 554 min
Histogram: 1 1 1 1 1 1 2 4 2 2
Nghost: 9033.81 ave 9096 max 8945 min
Histogram: 1 2 1 0 1 3 2 2 1 3
Neighs: 322465 ave 334797 max 311747 min
Histogram: 1 4 1 0 3 2 1 1 2 1
Total # of neighbors = 5159434
Ave neighs/atom = 561.54049
Ave special neighs/atom = 1.9037875
Neighbor list builds = 98972
Dangerous builds = 0
undump sci
restart 0
dump sci all custom 2000000 2.4.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) = 0.2557377
grid = 27 27 54
stencil order = 5
estimated absolute RMS force accuracy = 0.0032430487
estimated relative force accuracy = 9.7663448e-06
using double precision KISS FFT
3d grid and FFT values/proc = 8000 2916
generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 2000000
2 0.97 1.40185e-06 8436
2 103.7 0.000106286 2812
Per MPI rank memory allocation (min/avg/max) = 13.95 | 14.14 | 14.18 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 2129.478 93962.523 1.2789064 296.95398 52.106796 83.455533 0 0 19559.57 46218.761 -220.49494 -206915.39 -141001.49 5642.9167
Loop time of 8.35913e-06 on 16 procs for 0 steps with 9188 atoms
89.7% CPU use with 16 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 | | 8.359e-06 | | |100.00
Nlocal: 574.25 ave 588 max 554 min
Histogram: 1 1 1 1 1 1 2 4 2 2
Nghost: 9033.81 ave 9096 max 8945 min
Histogram: 1 2 1 0 1 3 2 2 1 3
Neighs: 322465 ave 334797 max 311747 min
Histogram: 1 4 1 0 3 2 1 1 2 1
Total # of neighbors = 5159434
Ave neighs/atom = 561.54049
Ave special neighs/atom = 1.9037875
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix shaken
log 2.5_NVT.out