./Stage_2/2.4_NVT.out output for 781: H2O-compress hou-nvt1ns-st2ns
Status:
finished
#-------------------------------------------------------------------------------
# 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 1 b 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
2200 = # 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 v_surfacetension 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 v_surfacetension 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) = 0.24368655
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.0034801097
estimated relative force accuracy = 1.0480247e-05
using double precision KISS FFT
3d grid and FFT values/proc = 15640 6048
generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 0
1 0.97 9.16378e-13 6600
1 103.7 8.42704e-11 2200
Per MPI rank memory allocation (min/avg/max) = 9.337 | 12.32 | 17.01 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 -114.50503 200895.44 0.32760043 301.09755 0 0 0 0 5564.9897 81661.013 -37.568224 -110321.96 -23095.953 3948.1667
SHAKE stats (type/ave/delta/count) on step 50000
1 0.97 1.25587e-06 6600
1 103.7 0.000104241 2200
SHAKE stats (type/ave/delta/count) on step 100000
1 0.97 1.18252e-06 6600
1 103.7 0.000114886 2200
SHAKE stats (type/ave/delta/count) on step 150000
1 0.97 1.31127e-06 6600
1 103.7 0.000117129 2200
SHAKE stats (type/ave/delta/count) on step 200000
1 0.97 1.53869e-06 6600
1 103.7 0.000105867 2200
SHAKE stats (type/ave/delta/count) on step 250000
1 0.97 1.25916e-06 6600
1 103.7 0.000104483 2200
SHAKE stats (type/ave/delta/count) on step 300000
1 0.97 1.33301e-06 6600
1 103.7 0.00010113 2200
SHAKE stats (type/ave/delta/count) on step 350000
1 0.97 1.36503e-06 6600
1 103.7 0.000113091 2200
SHAKE stats (type/ave/delta/count) on step 400000
1 0.97 1.69083e-06 6600
1 103.7 0.0001194 2200
SHAKE stats (type/ave/delta/count) on step 450000
1 0.97 1.40217e-06 6600
1 103.7 0.000107228 2200
SHAKE stats (type/ave/delta/count) on step 500000
1 0.97 1.26672e-06 6600
1 103.7 0.000101804 2200
SHAKE stats (type/ave/delta/count) on step 550000
1 0.97 1.48023e-06 6600
1 103.7 9.05e-05 2200
SHAKE stats (type/ave/delta/count) on step 600000
1 0.97 1.33572e-06 6600
1 103.7 9.50725e-05 2200
SHAKE stats (type/ave/delta/count) on step 650000
1 0.97 1.13869e-06 6600
1 103.7 0.000105917 2200
SHAKE stats (type/ave/delta/count) on step 700000
1 0.97 1.29195e-06 6600
1 103.7 0.000132032 2200
SHAKE stats (type/ave/delta/count) on step 750000
1 0.97 1.63206e-06 6600
1 103.7 0.000116686 2200
SHAKE stats (type/ave/delta/count) on step 800000
1 0.97 1.43677e-06 6600
1 103.7 0.000104104 2200
SHAKE stats (type/ave/delta/count) on step 850000
1 0.97 1.79925e-06 6600
1 103.7 0.000118407 2200
SHAKE stats (type/ave/delta/count) on step 900000
1 0.97 1.25183e-06 6600
1 103.7 0.000102399 2200
SHAKE stats (type/ave/delta/count) on step 950000
1 0.97 1.18511e-06 6600
1 103.7 0.000106887 2200
SHAKE stats (type/ave/delta/count) on step 1000000
1 0.97 1.24635e-06 6600
1 103.7 9.03713e-05 2200
SHAKE stats (type/ave/delta/count) on step 1050000
1 0.97 1.37475e-06 6600
1 103.7 0.000104646 2200
SHAKE stats (type/ave/delta/count) on step 1100000
1 0.97 1.3925e-06 6600
1 103.7 0.000109233 2200
SHAKE stats (type/ave/delta/count) on step 1150000
1 0.97 1.55089e-06 6600
1 103.7 0.000122741 2200
SHAKE stats (type/ave/delta/count) on step 1200000
1 0.97 1.6868e-06 6600
1 103.7 0.000133574 2200
SHAKE stats (type/ave/delta/count) on step 1250000
1 0.97 1.20349e-06 6600
1 103.7 8.93513e-05 2200
SHAKE stats (type/ave/delta/count) on step 1300000
1 0.97 1.1567e-06 6600
1 103.7 9.519e-05 2200
SHAKE stats (type/ave/delta/count) on step 1350000
1 0.97 1.63339e-06 6600
1 103.7 0.000111822 2200
SHAKE stats (type/ave/delta/count) on step 1400000
1 0.97 1.22358e-06 6600
1 103.7 0.000133079 2200
SHAKE stats (type/ave/delta/count) on step 1450000
1 0.97 1.51851e-06 6600
1 103.7 0.000121367 2200
SHAKE stats (type/ave/delta/count) on step 1500000
1 0.97 1.27499e-06 6600
1 103.7 0.000102146 2200
SHAKE stats (type/ave/delta/count) on step 1550000
1 0.97 1.52029e-06 6600
1 103.7 0.00011048 2200
SHAKE stats (type/ave/delta/count) on step 1600000
1 0.97 1.43115e-06 6600
1 103.7 0.000118661 2200
SHAKE stats (type/ave/delta/count) on step 1650000
1 0.97 1.60113e-06 6600
1 103.7 9.48277e-05 2200
SHAKE stats (type/ave/delta/count) on step 1700000
1 0.97 1.15681e-06 6600
1 103.7 9.15418e-05 2200
SHAKE stats (type/ave/delta/count) on step 1750000
1 0.97 1.14126e-06 6600
1 103.7 9.20236e-05 2200
SHAKE stats (type/ave/delta/count) on step 1800000
1 0.97 1.38395e-06 6600
1 103.7 0.000103406 2200
SHAKE stats (type/ave/delta/count) on step 1850000
1 0.97 1.83641e-06 6600
1 103.7 0.000139693 2200
SHAKE stats (type/ave/delta/count) on step 1900000
1 0.97 1.3489e-06 6600
1 103.7 0.000112539 2200
SHAKE stats (type/ave/delta/count) on step 1950000
1 0.97 1.09381e-06 6600
1 103.7 9.95394e-05 2200
SHAKE stats (type/ave/delta/count) on step 2000000
1 0.97 1.11002e-06 6600
1 103.7 9.4512e-05 2200
2000000 2000000 -94.906497 200895.44 0.32760043 292.52118 0 0 0 0 5616.8285 81583.79 -37.568224 -110317.05 -23116.434 3835.7083
Loop time of 76961.5 on 8 procs for 2000000 steps with 6600 atoms
Performance: 2.245 ns/day, 10.689 hours/ns, 25.987 timesteps/s
97.6% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.97823 | 20612 | 63149 |17900.8 | 26.78
Bond | 1.4174 | 2.5322 | 3.2089 | 34.2 | 0.00
Kspace | 8582.3 | 51190 | 71932 |11384.3 | 66.51
Neigh | 3551.5 | 3561.5 | 3571.4 | 15.6 | 4.63
Comm | 88.966 | 366.9 | 549.8 | 940.1 | 0.48
Output | 0.034888 | 0.036065 | 0.036992 | 0.4 | 0.00
Modify | 1072.6 | 1157 | 1296.2 | 254.3 | 1.50
Other | | 72.33 | | | 0.09
Nlocal: 825 ave 2264 max 0 min
Histogram: 4 0 0 0 2 0 0 0 0 2
Nghost: 5613.88 ave 11099 max 0 min
Histogram: 2 0 0 2 0 0 2 0 0 2
Neighs: 406604 ave 1.26402e+06 max 0 min
Histogram: 4 0 2 0 0 0 0 0 0 2
Total # of neighbors = 3252830
Ave neighs/atom = 492.85303
Ave special neighs/atom = 2
Neighbor list builds = 100038
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) = 0.24368655
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.0034801097
estimated relative force accuracy = 1.0480247e-05
using double precision KISS FFT
3d grid and FFT values/proc = 15640 6048
generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 2000000
1 0.97 1.11002e-06 6600
1 103.7 9.4512e-05 2200
Per MPI rank memory allocation (min/avg/max) = 9.334 | 12.43 | 17.01 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 -94.691415 200895.44 0.32760043 292.52118 0 0 0 0 5616.8285 81583.79 -37.568224 -110317.05 -23116.434 3835.7083
Loop time of 3.44925e-06 on 8 procs for 0 steps with 6600 atoms
101.5% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 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 | | 3.449e-06 | | |100.00
Nlocal: 825 ave 2264 max 0 min
Histogram: 4 0 0 0 2 0 0 0 0 2
Nghost: 5613.88 ave 11099 max 0 min
Histogram: 2 0 0 2 0 0 2 0 0 2
Neighs: 406604 ave 1.26402e+06 max 0 min
Histogram: 4 0 2 0 0 0 0 0 0 2
Total # of neighbors = 3252830
Ave neighs/atom = 492.85303
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix shaken
Total wall time: 32:52:34