#-------------------------------------------------------------------------------
# Stage 2.4: NPT integration for 3 ns with a timestep of 1 fs
# Temperature 298.2 K
# Pressure 1 atm
#-------------------------------------------------------------------------------
# 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
3563 = # of frozen angles
find clusters CPU = 0.001 seconds
change_box all triclinic
Changing box ...
triclinic box = (0 0 0) to (45.402 32.1502 97.6) with tilt (0 0 0)
kspace_style pppm 0.00001
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
change_box all triclinic
Changing box ...
triclinic box = (0 0 0) to (45.402 32.1502 97.6) with tilt (0 0 0)
fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 60000
fix 2 movable ave/time 1 299999 300000 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 300 1 300 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 3000000 2.4.restart
dump sci all custom 300000 2.4.xyz id mol type q xs ys zs
timestep 1
run 3000000
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 0.0384 (../kspace.cpp:325)
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.25851763
grid = 36 30 64
stencil order = 5
estimated absolute RMS force accuracy = 0.0028535172
estimated relative force accuracy = 8.5932824e-06
using double precision KISS FFT
3d grid and FFT values/proc = 8250 2160
generated 0 of 28 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 = 7 5 14
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/tri
stencil: half/bin/3d/tri
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
1 0.999749 0.679683 10689
1 97.9273 16.7474 3563
Per MPI rank memory allocation (min/avg/max) = 13.09 | 13.37 | 13.76 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 -2855.14 142465.1 1.3194986 420.52174 10.528927 31.665422 0 0 38035.562 -24893.603 -321.52187 -321734.59 -308550.44 10887.861
SHAKE stats (type/ave/delta/count) on step 50000
1 0.970096 0.000271305 10689
1 103.701 0.0310565 3563
SHAKE stats (type/ave/delta/count) on step 100000
1 0.969979 6.04533e-05 10689
1 103.7 0.0068798 3563
SHAKE stats (type/ave/delta/count) on step 150000
1 0.970013 3.59049e-05 10689
1 103.7 0.00407292 3563
SHAKE stats (type/ave/delta/count) on step 200000
1 0.969988 3.43469e-05 10689
1 103.7 0.00392 3563
SHAKE stats (type/ave/delta/count) on step 250000
1 0.970012 3.28104e-05 10689
1 103.7 0.00377722 3563
SHAKE stats (type/ave/delta/count) on step 300000
1 0.97008 0.000225157 10689
1 103.7 0.0257697 3563
SHAKE stats (type/ave/delta/count) on step 350000
1 0.96999 2.9231e-05 10689
1 103.7 0.00330985 3563
SHAKE stats (type/ave/delta/count) on step 400000
1 0.969968 9.21176e-05 10689
1 103.7 0.0104688 3563
SHAKE stats (type/ave/delta/count) on step 450000
1 0.970011 3.1106e-05 10689
1 103.7 0.00352861 3563
SHAKE stats (type/ave/delta/count) on step 500000
1 0.969973 7.76772e-05 10689
1 103.7 0.00885221 3563
SHAKE stats (type/ave/delta/count) on step 550000
1 0.969955 0.000129627 10689
1 103.7 0.0148299 3563
SHAKE stats (type/ave/delta/count) on step 600000
1 0.970043 0.000121988 10689
1 103.7 0.0139385 3563
SHAKE stats (type/ave/delta/count) on step 650000
1 0.970011 3.03044e-05 10689
1 103.7 0.0034581 3563
SHAKE stats (type/ave/delta/count) on step 700000
1 0.970038 0.000109338 10689
1 103.7 0.0125876 3563
SHAKE stats (type/ave/delta/count) on step 750000
1 0.970027 7.79885e-05 10689
1 103.7 0.00895959 3563
SHAKE stats (type/ave/delta/count) on step 800000
1 0.969964 0.000103009 10689
1 103.7 0.0117532 3563
SHAKE stats (type/ave/delta/count) on step 850000
1 0.969973 7.80547e-05 10689
1 103.7 0.00891043 3563
SHAKE stats (type/ave/delta/count) on step 900000
1 0.970002 7.05187e-06 10689
1 103.7 0.000799144 3563
SHAKE stats (type/ave/delta/count) on step 950000
1 0.970046 0.000128368 10689
1 103.7 0.0147489 3563
SHAKE stats (type/ave/delta/count) on step 1000000
1 0.970025 7.07494e-05 10689
1 103.7 0.00813736 3563
SHAKE stats (type/ave/delta/count) on step 1050000
1 0.969986 4.04744e-05 10689
1 103.7 0.00462281 3563
SHAKE stats (type/ave/delta/count) on step 1100000
1 0.970061 0.000174125 10689
1 103.7 0.0200007 3563
SHAKE stats (type/ave/delta/count) on step 1150000
1 0.969982 5.1324e-05 10689
1 103.7 0.00582603 3563
SHAKE stats (type/ave/delta/count) on step 1200000
1 0.969964 0.00010456 10689
1 103.7 0.0119605 3563
SHAKE stats (type/ave/delta/count) on step 1250000
1 0.970017 4.91934e-05 10689
1 103.7 0.00564262 3563
SHAKE stats (type/ave/delta/count) on step 1300000
1 0.970057 0.000161424 10689
1 103.7 0.0185256 3563
SHAKE stats (type/ave/delta/count) on step 1350000
1 0.970018 5.02702e-05 10689
1 103.7 0.0057513 3563
SHAKE stats (type/ave/delta/count) on step 1400000
1 0.969979 5.91696e-05 10689
1 103.7 0.0067535 3563
SHAKE stats (type/ave/delta/count) on step 1450000
1 0.969987 3.81678e-05 10689
1 103.7 0.00427478 3563
SHAKE stats (type/ave/delta/count) on step 1500000
1 0.970023 6.52404e-05 10689
1 103.7 0.00746965 3563
SHAKE stats (type/ave/delta/count) on step 1550000
1 0.969994 1.97356e-05 10689
1 103.7 0.00218743 3563
SHAKE stats (type/ave/delta/count) on step 1600000
1 0.970025 7.25822e-05 10689
1 103.7 0.00827384 3563
SHAKE stats (type/ave/delta/count) on step 1650000
1 0.970024 6.86082e-05 10689
1 103.7 0.00791519 3563
SHAKE stats (type/ave/delta/count) on step 1700000
1 0.970055 0.000155128 10689
1 103.7 0.017733 3563
SHAKE stats (type/ave/delta/count) on step 1750000
1 0.969981 5.46076e-05 10689
1 103.7 0.00619968 3563
SHAKE stats (type/ave/delta/count) on step 1800000
1 0.970021 5.80909e-05 10689
1 103.7 0.00666181 3563
SHAKE stats (type/ave/delta/count) on step 1850000
1 0.969965 0.000100749 10689
1 103.7 0.0114918 3563
SHAKE stats (type/ave/delta/count) on step 1900000
1 0.970016 4.58199e-05 10689
1 103.7 0.00521825 3563
SHAKE stats (type/ave/delta/count) on step 1950000
1 0.970018 5.15089e-05 10689
1 103.7 0.00590389 3563
SHAKE stats (type/ave/delta/count) on step 2000000
1 0.969987 3.80279e-05 10689
1 103.7 0.00432472 3563
SHAKE stats (type/ave/delta/count) on step 2050000
1 0.970036 0.000101726 10689
1 103.7 0.0116111 3563
SHAKE stats (type/ave/delta/count) on step 2100000
1 0.970017 4.85256e-05 10689
1 103.7 0.00552786 3563
SHAKE stats (type/ave/delta/count) on step 2150000
1 0.970008 2.20398e-05 10689
1 103.7 0.00252531 3563
SHAKE stats (type/ave/delta/count) on step 2200000
1 0.969973 7.93417e-05 10689
1 103.7 0.00904171 3563
SHAKE stats (type/ave/delta/count) on step 2250000
1 0.970024 6.92297e-05 10689
1 103.7 0.00789899 3563
SHAKE stats (type/ave/delta/count) on step 2300000
1 0.969973 7.72144e-05 10689
1 103.7 0.00877542 3563
SHAKE stats (type/ave/delta/count) on step 2350000
1 0.969981 5.45146e-05 10689
1 103.7 0.00623268 3563
SHAKE stats (type/ave/delta/count) on step 2400000
1 0.969978 6.32865e-05 10689
1 103.7 0.00720872 3563
SHAKE stats (type/ave/delta/count) on step 2450000
1 0.969987 3.85713e-05 10689
1 103.7 0.00433594 3563
SHAKE stats (type/ave/delta/count) on step 2500000
1 0.96995 0.000143344 10689
1 103.7 0.0163842 3563
SHAKE stats (type/ave/delta/count) on step 2550000
1 0.969968 9.2659e-05 10689
1 103.7 0.0105502 3563
SHAKE stats (type/ave/delta/count) on step 2600000
1 0.969975 7.31493e-05 10689
1 103.7 0.00831851 3563
SHAKE stats (type/ave/delta/count) on step 2650000
1 0.970045 0.00012765 10689
1 103.7 0.0146433 3563
SHAKE stats (type/ave/delta/count) on step 2700000
1 0.969988 3.44024e-05 10689
1 103.7 0.00391034 3563
SHAKE stats (type/ave/delta/count) on step 2750000
1 0.969953 0.000135377 10689
1 103.7 0.0154767 3563
SHAKE stats (type/ave/delta/count) on step 2800000
1 0.969955 0.000128387 10689
1 103.7 0.0146687 3563
SHAKE stats (type/ave/delta/count) on step 2850000
1 0.969968 9.19759e-05 10689
1 103.7 0.0105146 3563
SHAKE stats (type/ave/delta/count) on step 2900000
1 0.970003 9.79208e-06 10689
1 103.7 0.00110293 3563
SHAKE stats (type/ave/delta/count) on step 2950000
1 0.970021 5.90911e-05 10689
1 103.7 0.00681709 3563
SHAKE stats (type/ave/delta/count) on step 3000000
1 0.970034 9.72951e-05 10689
1 103.7 0.0111611 3563
3000000 3000000 247.93187 138549.81 1.3567865 297.96756 33.217022 55.412594 0 0 37312.54 -9708.8524 -330.60779 -321736.35 -294044.03 7714.7722
Loop time of 32399.8 on 32 procs for 3000000 steps with 12250 atoms
Performance: 8.000 ns/day, 3.000 hours/ns, 92.593 timesteps/s
99.3% CPU use with 32 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13396 | 16959 | 19395 |1605.1 | 52.34
Bond | 3.2864 | 8.0126 | 16.133 | 122.6 | 0.02
Kspace | 6149.3 | 8582.8 | 12155 |2265.5 | 26.49
Neigh | 1522.8 | 1525.3 | 1527.5 | 3.3 | 4.71
Comm | 1660.1 | 1802.8 | 1884.4 | 173.8 | 5.56
Output | 0.012566 | 0.015346 | 0.017957 | 1.3 | 0.00
Modify | 3175.9 | 3253.5 | 3493.7 | 153.6 | 10.04
Other | | 267.9 | | | 0.83
Nlocal: 382.812 ave 421 max 330 min
Histogram: 3 4 1 0 2 4 2 8 3 5
Nghost: 7471.47 ave 7922 max 6973 min
Histogram: 8 0 0 6 2 0 4 3 1 8
Neighs: 195078 ave 228320 max 149203 min
Histogram: 3 5 0 0 1 5 3 5 6 4
Total # of neighbors = 6242492
Ave neighs/atom = 509.59118
Ave special neighs/atom = 1.7892245
Neighbor list builds = 160431
Dangerous builds = 0
undump sci
restart 0
dump sci all custom 3000000 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) = 0.25733669
grid = 36 30 60
stencil order = 5
estimated absolute RMS force accuracy = 0.0031614499
estimated relative force accuracy = 9.5206124e-06
using double precision KISS FFT
3d grid and FFT values/proc = 7700 2160
generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 3000000
1 0.970034 9.72951e-05 10689
1 103.7 0.0111611 3563
Per MPI rank memory allocation (min/avg/max) = 13.07 | 13.51 | 13.75 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
3000000 3000000 428.55255 138549.81 1.3567865 297.96756 33.217022 55.412594 0 0 37312.54 -11163.718 -330.60779 -320281.16 -294043.7 7714.7722
Loop time of 1.03691e-05 on 32 procs for 0 steps with 12250 atoms
116.9% CPU use with 32 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 | | 1.037e-05 | | |100.00
Nlocal: 382.812 ave 421 max 330 min
Histogram: 3 4 1 0 2 4 2 8 3 5
Nghost: 7471.47 ave 7922 max 6973 min
Histogram: 8 0 0 6 2 0 4 3 1 8
Neighs: 195078 ave 228320 max 149203 min
Histogram: 3 5 0 0 1 5 3 5 6 4
Total # of neighbors = 6242492
Ave neighs/atom = 509.59118
Ave special neighs/atom = 1.7892245
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix shaken
log 2.5_NVT.out