./Stage_2/2.3_NVT.out output for 781: H2O-compress hou-nvt1ns-st2ns
Status:
finished
#-------------------------------------------------------------------------------
# Stage 2.3: NVT integration for 1 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
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888)
thermo ${Nthermo}
thermo 0
fix 1 movable nvt temp 298.2 298.2 100 drag 0.0
fix 2 movable ave/time 1 100000 100000 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 2.3_averages.txt off 1
fix 3 movable ave/time 100 1 100 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 2.3_instantaneous.txt
restart 1000000 2.3.restart
dump sci all custom 100000 2.3.xyz id mol type q xs ys zs
timestep 1
run 1000000
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
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 18
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
1 0.996267 0.0531421 6600
1 98.4561 11.5015 2200
Per MPI rank memory allocation (min/avg/max) = 9.216 | 12.05 | 17 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 -837.55836 200895.44 0.32760043 447.33389 0 0 0 0 6274.0189 73639.171 -37.568224 -110345.64 -30432.447 5865.703
SHAKE stats (type/ave/delta/count) on step 50000
1 0.97 1.25208e-06 6600
1 103.7 0.000100376 2200
SHAKE stats (type/ave/delta/count) on step 100000
1 0.97 1.3521e-06 6600
1 103.7 0.000101948 2200
SHAKE stats (type/ave/delta/count) on step 150000
1 0.97 1.28549e-06 6600
1 103.7 0.000106053 2200
SHAKE stats (type/ave/delta/count) on step 200000
1 0.97 1.2371e-06 6600
1 103.7 9.91953e-05 2200
SHAKE stats (type/ave/delta/count) on step 250000
1 0.97 1.32533e-06 6600
1 103.7 0.000102024 2200
SHAKE stats (type/ave/delta/count) on step 300000
1 0.97 1.33477e-06 6600
1 103.7 9.59069e-05 2200
SHAKE stats (type/ave/delta/count) on step 350000
1 0.97 1.37529e-06 6600
1 103.7 8.89976e-05 2200
SHAKE stats (type/ave/delta/count) on step 400000
1 0.97 1.40585e-06 6600
1 103.7 0.000131919 2200
SHAKE stats (type/ave/delta/count) on step 450000
1 0.97 1.15759e-06 6600
1 103.7 0.000112036 2200
SHAKE stats (type/ave/delta/count) on step 500000
1 0.97 1.32885e-06 6600
1 103.7 0.000113807 2200
SHAKE stats (type/ave/delta/count) on step 550000
1 0.97 1.13202e-06 6600
1 103.7 9.06406e-05 2200
SHAKE stats (type/ave/delta/count) on step 600000
1 0.97 1.32123e-06 6600
1 103.7 0.000110148 2200
SHAKE stats (type/ave/delta/count) on step 650000
1 0.97 1.23364e-06 6600
1 103.7 0.000101235 2200
SHAKE stats (type/ave/delta/count) on step 700000
1 0.97 1.25127e-06 6600
1 103.7 0.000103783 2200
SHAKE stats (type/ave/delta/count) on step 750000
1 0.97 1.21873e-06 6600
1 103.7 0.00010092 2200
SHAKE stats (type/ave/delta/count) on step 800000
1 0.97 1.13877e-06 6600
1 103.7 0.00010081 2200
SHAKE stats (type/ave/delta/count) on step 850000
1 0.97 1.58497e-06 6600
1 103.7 0.000104804 2200
SHAKE stats (type/ave/delta/count) on step 900000
1 0.97 1.15417e-06 6600
1 103.7 9.91624e-05 2200
SHAKE stats (type/ave/delta/count) on step 950000
1 0.97 1.46089e-06 6600
1 103.7 0.000111068 2200
SHAKE stats (type/ave/delta/count) on step 1000000
1 0.97 1.48144e-06 6600
1 103.7 0.000105723 2200
1000000 1000000 -114.68054 200895.44 0.32760043 301.09755 0 0 0 0 5564.9899 81660.995 -37.568224 -110321.96 -23095.97 3948.1667
Loop time of 41392.8 on 8 procs for 1000000 steps with 6600 atoms
Performance: 2.087 ns/day, 11.498 hours/ns, 24.159 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 | 0.56736 | 11272 | 33654 |12744.3 | 27.23
Bond | 0.81681 | 1.5796 | 2.2149 | 37.1 | 0.00
Kspace | 4952.9 | 27369 | 38715 |8199.4 | 66.12
Neigh | 1880.6 | 1886.7 | 1892 | 11.5 | 4.56
Comm | 45.612 | 208.32 | 313.74 | 729.1 | 0.50
Output | 0.036323 | 0.037622 | 0.038698 | 0.5 | 0.00
Modify | 569.16 | 617.81 | 702.1 | 214.1 | 1.49
Other | | 37.45 | | | 0.09
Nlocal: 825 ave 2292 max 0 min
Histogram: 4 0 0 0 2 0 0 0 0 2
Nghost: 5623.38 ave 11098 max 0 min
Histogram: 2 0 0 2 0 0 2 0 0 2
Neighs: 405941 ave 1.29276e+06 max 0 min
Histogram: 4 0 2 0 0 0 0 0 0 2
Total # of neighbors = 3247526
Ave neighs/atom = 492.04939
Ave special neighs/atom = 2
Neighbor list builds = 50025
Dangerous builds = 0
undump sci
restart 0
dump sci all custom 1000000 2.3.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 1000000
1 0.97 1.48144e-06 6600
1 103.7 0.000105723 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
1000000 1000000 -114.50992 200895.44 0.32760043 301.09755 0 0 0 0 5564.9899 81660.995 -37.568224 -110321.96 -23095.97 3948.1667
Loop time of 4.4635e-06 on 8 procs for 0 steps with 6600 atoms
117.6% 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 | 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 | | 4.464e-06 | | |100.00
Nlocal: 825 ave 2292 max 0 min
Histogram: 4 0 0 0 2 0 0 0 0 2
Nghost: 5623.38 ave 11098 max 0 min
Histogram: 2 0 0 2 0 0 2 0 0 2
Neighs: 405941 ave 1.29276e+06 max 0 min
Histogram: 4 0 2 0 0 0 0 0 0 2
Total # of neighbors = 3247526
Ave neighs/atom = 492.04939
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix shaken
log 2.4_NVT.out