./Stage_2/2.4_NVT.out output for 779: Na2SO4-1m-NVT 1ns-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
2109 = # 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) = 0.24383926
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.0037486683
estimated relative force accuracy = 1.1289003e-05
using double precision KISS FFT
3d grid and FFT values/proc = 15640 6048
generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 0
1 0.97 1.07536e-12 6327
1 103.7 9.34506e-11 2109
Per MPI rank memory allocation (min/avg/max) = 11.96 | 14.7 | 18.29 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 -282.01652 199494.69 0.36118278 303.94829 54.268523 80.036408 0 0 6214.4646 72251.604 -42.647801 -119676.16 -41075.786 4061.6523
SHAKE stats (type/ave/delta/count) on step 50000
1 0.97 1.11984e-06 6327
1 103.7 9.32494e-05 2109
SHAKE stats (type/ave/delta/count) on step 100000
1 0.97 1.52824e-06 6327
1 103.7 0.000106103 2109
SHAKE stats (type/ave/delta/count) on step 150000
1 0.97 1.47005e-06 6327
1 103.7 0.000144854 2109
SHAKE stats (type/ave/delta/count) on step 200000
1 0.97 1.4251e-06 6327
1 103.7 0.00012464 2109
SHAKE stats (type/ave/delta/count) on step 250000
1 0.97 1.17629e-06 6327
1 103.7 9.71878e-05 2109
SHAKE stats (type/ave/delta/count) on step 300000
1 0.97 1.26536e-06 6327
1 103.7 0.000105256 2109
SHAKE stats (type/ave/delta/count) on step 350000
1 0.97 1.11373e-06 6327
1 103.7 0.000100148 2109
SHAKE stats (type/ave/delta/count) on step 400000
1 0.97 1.45348e-06 6327
1 103.7 0.000122969 2109
SHAKE stats (type/ave/delta/count) on step 450000
1 0.97 1.24133e-06 6327
1 103.7 9.42631e-05 2109
SHAKE stats (type/ave/delta/count) on step 500000
1 0.97 1.34821e-06 6327
1 103.7 0.000131116 2109
SHAKE stats (type/ave/delta/count) on step 550000
1 0.97 1.28575e-06 6327
1 103.7 0.000105992 2109
SHAKE stats (type/ave/delta/count) on step 600000
1 0.97 1.23081e-06 6327
1 103.7 9.73771e-05 2109
SHAKE stats (type/ave/delta/count) on step 650000
1 0.97 1.29761e-06 6327
1 103.7 8.98615e-05 2109
SHAKE stats (type/ave/delta/count) on step 700000
1 0.97 1.11441e-06 6327
1 103.7 9.01013e-05 2109
SHAKE stats (type/ave/delta/count) on step 750000
1 0.97 1.16024e-06 6327
1 103.7 0.000101711 2109
SHAKE stats (type/ave/delta/count) on step 800000
1 0.97 1.36185e-06 6327
1 103.7 0.000142095 2109
SHAKE stats (type/ave/delta/count) on step 850000
1 0.97 1.28255e-06 6327
1 103.7 0.000103467 2109
SHAKE stats (type/ave/delta/count) on step 900000
1 0.97 1.28122e-06 6327
1 103.7 9.76645e-05 2109
SHAKE stats (type/ave/delta/count) on step 950000
1 0.97 1.29535e-06 6327
1 103.7 0.000107235 2109
SHAKE stats (type/ave/delta/count) on step 1000000
1 0.97 1.34664e-06 6327
1 103.7 9.91936e-05 2109
SHAKE stats (type/ave/delta/count) on step 1050000
1 0.97 1.19889e-06 6327
1 103.7 0.000107349 2109
SHAKE stats (type/ave/delta/count) on step 1100000
1 0.97 1.66547e-06 6327
1 103.7 0.000124866 2109
SHAKE stats (type/ave/delta/count) on step 1150000
1 0.97 1.52286e-06 6327
1 103.7 0.000112539 2109
SHAKE stats (type/ave/delta/count) on step 1200000
1 0.97 1.75092e-06 6327
1 103.7 9.41799e-05 2109
SHAKE stats (type/ave/delta/count) on step 1250000
1 0.97 1.23436e-06 6327
1 103.7 9.51558e-05 2109
SHAKE stats (type/ave/delta/count) on step 1300000
1 0.97 1.603e-06 6327
1 103.7 0.000104586 2109
SHAKE stats (type/ave/delta/count) on step 1350000
1 0.97 1.87671e-06 6327
1 103.7 0.000128285 2109
SHAKE stats (type/ave/delta/count) on step 1400000
1 0.97 1.21609e-06 6327
1 103.7 9.94305e-05 2109
SHAKE stats (type/ave/delta/count) on step 1450000
1 0.97 1.30937e-06 6327
1 103.7 9.39489e-05 2109
SHAKE stats (type/ave/delta/count) on step 1500000
1 0.97 1.21494e-06 6327
1 103.7 9.25808e-05 2109
SHAKE stats (type/ave/delta/count) on step 1550000
1 0.97 1.38048e-06 6327
1 103.7 0.000107471 2109
SHAKE stats (type/ave/delta/count) on step 1600000
1 0.97 1.68077e-06 6327
1 103.7 0.000102922 2109
SHAKE stats (type/ave/delta/count) on step 1650000
1 0.97 1.33463e-06 6327
1 103.7 9.71105e-05 2109
SHAKE stats (type/ave/delta/count) on step 1700000
1 0.97 1.25909e-06 6327
1 103.7 0.000116977 2109
SHAKE stats (type/ave/delta/count) on step 1750000
1 0.97 1.31459e-06 6327
1 103.7 0.000103129 2109
SHAKE stats (type/ave/delta/count) on step 1800000
1 0.97 1.29102e-06 6327
1 103.7 0.000104397 2109
SHAKE stats (type/ave/delta/count) on step 1850000
1 0.97 1.23274e-06 6327
1 103.7 9.12009e-05 2109
SHAKE stats (type/ave/delta/count) on step 1900000
1 0.97 1.32871e-06 6327
1 103.7 9.12531e-05 2109
SHAKE stats (type/ave/delta/count) on step 1950000
1 0.97 1.18346e-06 6327
1 103.7 0.000117879 2109
SHAKE stats (type/ave/delta/count) on step 2000000
1 0.97 1.52421e-06 6327
1 103.7 0.000121572 2109
2000000 2000000 -183.29492 199494.69 0.36118278 296.67502 62.149629 80.071213 0 0 6086.4027 72420.723 -42.647801 -119687.17 -41037.825 3964.4598
Loop time of 74354.5 on 8 procs for 2000000 steps with 6593 atoms
Performance: 2.324 ns/day, 10.327 hours/ns, 26.898 timesteps/s
97.8% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3625 | 22635 | 60816 |16309.2 | 30.44
Bond | 1.7071 | 11.889 | 38.648 | 369.4 | 0.02
Kspace | 8343.2 | 46590 | 69277 |11394.7 | 62.66
Neigh | 3467.2 | 3476.6 | 3490.1 | 15.5 | 4.68
Comm | 212.77 | 407.94 | 598.26 | 898.1 | 0.55
Output | 0.032648 | 0.034802 | 0.036169 | 0.6 | 0.00
Modify | 1037.5 | 1162.3 | 1287 | 348.3 | 1.56
Other | | 70.86 | | | 0.10
Nlocal: 824.125 ave 1935 max 0 min
Histogram: 4 0 0 0 0 0 0 2 0 2
Nghost: 5494.62 ave 10567 max 314 min
Histogram: 2 2 0 0 0 0 0 0 2 2
Neighs: 411536 ave 1.08667e+06 max 0 min
Histogram: 4 0 0 0 0 2 0 0 0 2
Total # of neighbors = 3292290
Ave neighs/atom = 499.36144
Ave special neighs/atom = 2.0345821
Neighbor list builds = 99432
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) = 0.24383926
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.0037486683
estimated relative force accuracy = 1.1289003e-05
using double precision KISS FFT
3d grid and FFT values/proc = 15640 6048
generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 2000000
1 0.97 1.52421e-06 6327
1 103.7 0.000121572 2109
Per MPI rank memory allocation (min/avg/max) = 11.98 | 14.71 | 18.28 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 -183.04648 199494.69 0.36118278 296.67502 62.149629 80.071213 0 0 6086.4027 72420.723 -42.647801 -119687.17 -41037.825 3964.4598
Loop time of 3.952e-06 on 8 procs for 0 steps with 6593 atoms
123.4% 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 | | 3.952e-06 | | |100.00
Nlocal: 824.125 ave 1935 max 0 min
Histogram: 4 0 0 0 0 0 0 2 0 2
Nghost: 5494.62 ave 10567 max 314 min
Histogram: 2 2 0 0 0 0 0 0 2 2
Neighs: 411536 ave 1.08667e+06 max 0 min
Histogram: 4 0 0 0 0 2 0 0 0 2
Total # of neighbors = 3292290
Ave neighs/atom = 499.36144
Ave special neighs/atom = 2.0345821
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix shaken
Total wall time: 32:05:49