./Stage_2/2.4_NPT.out output for 780: Na2SO4-0.5m-step 1-npt2ns-nvt2ns
Status:
finished
#-------------------------------------------------------------------------------
# Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs
# Temperature 298.2 K
# Pressure 1 bar
#-------------------------------------------------------------------------------
# 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
2220 = # 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 npt temp 298.2 298.2 100 iso 0.9869233 0.9869233 100 drag 0 mtk yes nreset 40000
fix 2 movable ave/time 1 199999 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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) = 0.2552295
grid = 30 30 30
stencil order = 5
estimated absolute RMS force accuracy = 0.0027755785
estimated relative force accuracy = 8.3585721e-06
using double precision KISS FFT
3d grid and FFT values/proc = 10648 3600
generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 0
1 0.999995 0.0726589 6660
1 97.8729 12.7009 2220
Per MPI rank memory allocation (min/avg/max) = 14.64 | 14.95 | 15.24 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 -2631.6171 67280.441 1.0572025 442.77392 4.3276681 10.395598 0 0 10328.066 69390.168 -126.84101 -124268.38 -44535.427 6043.4785
SHAKE stats (type/ave/delta/count) on step 50000
1 0.97005 1.4892e-06 6660
1 103.7 0.000102598 2220
SHAKE stats (type/ave/delta/count) on step 100000
1 0.970015 1.13159e-06 6660
1 103.7 0.000110648 2220
SHAKE stats (type/ave/delta/count) on step 150000
1 0.969954 1.2119e-06 6660
1 103.7 0.000125579 2220
SHAKE stats (type/ave/delta/count) on step 200000
1 0.97 1.43989e-06 6660
1 103.7 0.000107289 2220
SHAKE stats (type/ave/delta/count) on step 250000
1 0.970081 1.4126e-06 6660
1 103.7 0.000108784 2220
SHAKE stats (type/ave/delta/count) on step 300000
1 0.969938 1.51416e-06 6660
1 103.7 0.000114561 2220
SHAKE stats (type/ave/delta/count) on step 350000
1 0.970084 1.6017e-06 6660
1 103.7 0.000134648 2220
SHAKE stats (type/ave/delta/count) on step 400000
1 0.970024 1.24902e-06 6660
1 103.7 8.90812e-05 2220
SHAKE stats (type/ave/delta/count) on step 450000
1 0.970043 1.28235e-06 6660
1 103.7 9.958e-05 2220
SHAKE stats (type/ave/delta/count) on step 500000
1 0.970006 1.38442e-06 6660
1 103.7 0.000110743 2220
SHAKE stats (type/ave/delta/count) on step 550000
1 0.969999 1.23888e-06 6660
1 103.7 0.000121445 2220
SHAKE stats (type/ave/delta/count) on step 600000
1 0.970044 2.01459e-06 6660
1 103.7 0.000117475 2220
SHAKE stats (type/ave/delta/count) on step 650000
1 0.970119 2.23312e-06 6660
1 103.7 0.000159218 2220
SHAKE stats (type/ave/delta/count) on step 700000
1 0.969949 1.26577e-06 6660
1 103.7 0.000139195 2220
SHAKE stats (type/ave/delta/count) on step 750000
1 0.969875 1.445e-06 6660
1 103.7 0.000114115 2220
SHAKE stats (type/ave/delta/count) on step 800000
1 0.970038 1.25262e-06 6660
1 103.7 0.000100318 2220
SHAKE stats (type/ave/delta/count) on step 850000
1 0.969998 1.10063e-06 6660
1 103.7 9.8467e-05 2220
SHAKE stats (type/ave/delta/count) on step 900000
1 0.969971 1.26752e-06 6660
1 103.7 0.000100938 2220
SHAKE stats (type/ave/delta/count) on step 950000
1 0.97005 1.43916e-06 6660
1 103.7 9.2492e-05 2220
SHAKE stats (type/ave/delta/count) on step 1000000
1 0.970036 1.57921e-06 6660
1 103.7 9.90835e-05 2220
SHAKE stats (type/ave/delta/count) on step 1050000
1 0.969957 1.16735e-06 6660
1 103.7 9.73839e-05 2220
SHAKE stats (type/ave/delta/count) on step 1100000
1 0.969949 1.24748e-06 6660
1 103.7 9.05714e-05 2220
SHAKE stats (type/ave/delta/count) on step 1150000
1 0.969974 1.48297e-06 6660
1 103.7 0.000115756 2220
SHAKE stats (type/ave/delta/count) on step 1200000
1 0.969923 1.29575e-06 6660
1 103.7 0.000125229 2220
SHAKE stats (type/ave/delta/count) on step 1250000
1 0.969984 1.2737e-06 6660
1 103.7 0.000107774 2220
SHAKE stats (type/ave/delta/count) on step 1300000
1 0.970059 1.22214e-06 6660
1 103.7 9.92316e-05 2220
SHAKE stats (type/ave/delta/count) on step 1350000
1 0.970074 1.15338e-06 6660
1 103.7 9.60975e-05 2220
SHAKE stats (type/ave/delta/count) on step 1400000
1 0.970108 1.47428e-06 6660
1 103.7 0.000108197 2220
SHAKE stats (type/ave/delta/count) on step 1450000
1 0.969979 1.28654e-06 6660
1 103.7 9.00507e-05 2220
SHAKE stats (type/ave/delta/count) on step 1500000
1 0.969967 1.21455e-06 6660
1 103.7 0.000103512 2220
SHAKE stats (type/ave/delta/count) on step 1550000
1 0.970052 1.3299e-06 6660
1 103.7 9.82706e-05 2220
SHAKE stats (type/ave/delta/count) on step 1600000
1 0.969959 1.23145e-06 6660
1 103.7 0.000104671 2220
SHAKE stats (type/ave/delta/count) on step 1650000
1 0.969938 1.26378e-06 6660
1 103.7 0.000105168 2220
SHAKE stats (type/ave/delta/count) on step 1700000
1 0.970061 1.63167e-06 6660
1 103.7 0.000114514 2220
SHAKE stats (type/ave/delta/count) on step 1750000
1 0.970003 1.2018e-06 6660
1 103.7 0.000133554 2220
SHAKE stats (type/ave/delta/count) on step 1800000
1 0.970058 1.31601e-06 6660
1 103.7 0.000107636 2220
SHAKE stats (type/ave/delta/count) on step 1850000
1 0.970053 1.25099e-06 6660
1 103.7 9.51458e-05 2220
SHAKE stats (type/ave/delta/count) on step 1900000
1 0.969975 1.168e-06 6660
1 103.7 9.64609e-05 2220
SHAKE stats (type/ave/delta/count) on step 1950000
1 0.969965 1.27539e-06 6660
1 103.7 0.000109841 2220
SHAKE stats (type/ave/delta/count) on step 2000000
1 0.969993 1.18255e-06 6660
1 103.7 9.76036e-05 2220
2000000 2000000 -266.48195 67356.279 1.0560122 301.19653 31.874342 43.810725 0 0 6141.8403 84228.534 -126.69819 -124247.3 -33801.246 4111.0704
Loop time of 42695.7 on 8 procs for 2000000 steps with 6800 atoms
Performance: 4.047 ns/day, 5.930 hours/ns, 46.843 timesteps/s
98.8% CPU use with 8 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 24774 | 27099 | 33916 |1663.2 | 63.47
Bond | 7.6276 | 9.826 | 12.602 | 43.7 | 0.02
Kspace | 4150.9 | 10974 | 13300 |2615.1 | 25.70
Neigh | 1892.5 | 1893.8 | 1894.5 | 1.7 | 4.44
Comm | 505.04 | 511.65 | 518.86 | 18.0 | 1.20
Output | 0.020632 | 0.021708 | 0.022632 | 0.5 | 0.00
Modify | 1665.3 | 1884.8 | 2141.8 | 322.3 | 4.41
Other | | 323.2 | | | 0.76
Nlocal: 850 ave 877 max 826 min
Histogram: 1 2 0 0 1 0 3 0 0 1
Nghost: 10516.5 ave 10586 max 10463 min
Histogram: 2 0 0 2 0 2 1 0 0 1
Neighs: 492767 ave 528747 max 460888 min
Histogram: 2 0 1 0 1 2 0 0 0 2
Total # of neighbors = 3942135
Ave neighs/atom = 579.72574
Ave special neighs/atom = 2.0176471
Neighbor list builds = 103312
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) = 0.25520686
grid = 30 30 30
stencil order = 5
estimated absolute RMS force accuracy = 0.0027786767
estimated relative force accuracy = 8.3679023e-06
using double precision KISS FFT
3d grid and FFT values/proc = 10648 3600
generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 2000000
1 0.969993 1.18255e-06 6660
1 103.7 9.76036e-05 2220
Per MPI rank memory allocation (min/avg/max) = 15.23 | 15.24 | 15.26 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 -314.50139 67356.279 1.0560122 301.19653 31.874342 43.810725 0 0 6141.8403 84217.525 -126.69819 -124236.3 -33801.246 4111.0704
Loop time of 3.23713e-06 on 8 procs for 0 steps with 6800 atoms
127.4% 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 | | 3.237e-06 | | |100.00
Nlocal: 850 ave 877 max 826 min
Histogram: 1 2 0 0 1 0 3 0 0 1
Nghost: 10516.5 ave 10586 max 10463 min
Histogram: 2 0 0 2 0 2 1 0 0 1
Neighs: 492767 ave 528747 max 460888 min
Histogram: 2 0 1 0 1 2 0 0 0 2
Total # of neighbors = 3942135
Ave neighs/atom = 579.72574
Ave special neighs/atom = 2.0176471
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix shaken
log 2.5_NVT.out