./Stage_2/2.3_NVT.out output for 779: Na2SO4-1m-NVT 1ns-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
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
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) = 0.24383926
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
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 0.97 9.79212e-05 6327
1 103.7 0.00779302 2109
Per MPI rank memory allocation (min/avg/max) = 11.8 | 14.49 | 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
0 1e-06 1191.64 199494.69 0.36118278 438.48637 59.478405 85.640776 0 0 6326.3231 72693.505 -42.647801 -119527.25 -40362.303 5859.4809
SHAKE stats (type/ave/delta/count) on step 50000
1 0.97 1.4899e-06 6327
1 103.7 0.000118281 2109
SHAKE stats (type/ave/delta/count) on step 100000
1 0.97 1.16711e-06 6327
1 103.7 0.000101322 2109
SHAKE stats (type/ave/delta/count) on step 150000
1 0.97 1.23331e-06 6327
1 103.7 0.000102156 2109
SHAKE stats (type/ave/delta/count) on step 200000
1 0.97 1.12988e-06 6327
1 103.7 0.000105241 2109
SHAKE stats (type/ave/delta/count) on step 250000
1 0.97 1.1683e-06 6327
1 103.7 9.47322e-05 2109
SHAKE stats (type/ave/delta/count) on step 300000
1 0.97 1.25785e-06 6327
1 103.7 0.000136076 2109
SHAKE stats (type/ave/delta/count) on step 350000
1 0.97 1.47509e-06 6327
1 103.7 0.000113316 2109
SHAKE stats (type/ave/delta/count) on step 400000
1 0.97 1.20928e-06 6327
1 103.7 8.94236e-05 2109
SHAKE stats (type/ave/delta/count) on step 450000
1 0.97 1.19849e-06 6327
1 103.7 9.59275e-05 2109
SHAKE stats (type/ave/delta/count) on step 500000
1 0.97 1.40206e-06 6327
1 103.7 9.71755e-05 2109
SHAKE stats (type/ave/delta/count) on step 550000
1 0.97 1.08258e-06 6327
1 103.7 8.84031e-05 2109
SHAKE stats (type/ave/delta/count) on step 600000
1 0.97 1.38675e-06 6327
1 103.7 0.000106532 2109
SHAKE stats (type/ave/delta/count) on step 650000
1 0.97 1.37396e-06 6327
1 103.7 0.000102127 2109
SHAKE stats (type/ave/delta/count) on step 700000
1 0.97 1.24756e-06 6327
1 103.7 9.76315e-05 2109
SHAKE stats (type/ave/delta/count) on step 750000
1 0.97 1.18459e-06 6327
1 103.7 9.09482e-05 2109
SHAKE stats (type/ave/delta/count) on step 800000
1 0.97 1.23946e-06 6327
1 103.7 9.38594e-05 2109
SHAKE stats (type/ave/delta/count) on step 850000
1 0.97 1.144e-06 6327
1 103.7 9.60156e-05 2109
SHAKE stats (type/ave/delta/count) on step 900000
1 0.97 1.18083e-06 6327
1 103.7 9.79503e-05 2109
SHAKE stats (type/ave/delta/count) on step 950000
1 0.97 1.37683e-06 6327
1 103.7 9.54331e-05 2109
SHAKE stats (type/ave/delta/count) on step 1000000
1 0.97 1.43339e-06 6327
1 103.7 9.97838e-05 2109
1000000 1000000 -282.27204 199494.69 0.36118278 303.94829 54.268523 80.036408 0 0 6214.4647 72251.583 -42.647801 -119676.16 -41075.808 4061.6523
Loop time of 41195 on 8 procs for 1000000 steps with 6593 atoms
Performance: 2.097 ns/day, 11.443 hours/ns, 24.275 timesteps/s
97.7% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6271 | 11932 | 34274 |12013.7 | 28.96
Bond | 0.89606 | 6.263 | 18.524 | 238.5 | 0.02
Kspace | 4066.4 | 26443 | 38403 |8089.0 | 64.19
Neigh | 1916.9 | 1922.2 | 1929.2 | 10.9 | 4.67
Comm | 115.33 | 225.07 | 337.2 | 687.5 | 0.55
Output | 0.035325 | 0.037299 | 0.038622 | 0.5 | 0.00
Modify | 554.06 | 628.92 | 702.32 | 278.0 | 1.53
Other | | 37.94 | | | 0.09
Nlocal: 824.125 ave 1984 max 0 min
Histogram: 4 0 0 0 0 0 1 1 0 2
Nghost: 5498.88 ave 10648 max 179 min
Histogram: 2 0 2 0 0 0 0 0 2 2
Neighs: 408296 ave 1.09261e+06 max 0 min
Histogram: 4 0 0 0 1 1 0 0 0 2
Total # of neighbors = 3266364
Ave neighs/atom = 495.42909
Ave special neighs/atom = 2.0345821
Neighbor list builds = 49684
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) = 0.24383926
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 1000000
1 0.97 1.43339e-06 6327
1 103.7 9.97838e-05 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
1000000 1000000 -282.02256 199494.69 0.36118278 303.94829 54.268523 80.036408 0 0 6214.4647 72251.583 -42.647801 -119676.16 -41075.808 4061.6523
Loop time of 3.97138e-06 on 8 procs for 0 steps with 6593 atoms
119.6% 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 | | 3.971e-06 | | |100.00
Nlocal: 824.125 ave 1984 max 0 min
Histogram: 4 0 0 0 0 0 1 1 0 2
Nghost: 5498.88 ave 10648 max 179 min
Histogram: 2 0 2 0 0 0 0 0 2 2
Neighs: 408296 ave 1.09261e+06 max 0 min
Histogram: 4 0 0 0 1 1 0 0 0 2
Total # of neighbors = 3266364
Ave neighs/atom = 495.42909
Ave special neighs/atom = 2.0345821
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix shaken
log 2.4_NVT.out