#-------------------------------------------------------------------------------
# Stage 2.4: NVT integration for 10 ps 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 2 b 2
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
2812 = # 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 1000 1000 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 2.4_averages.txt off 1
fix 3 movable ave/time 1 1 1 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 2.4_instantaneous.txt
fix 4 fixed setforce 0.0 0.0 0.0
restart 10000 2.4.restart
dump sci all custom 1000 2.4.xyz id mol type q xs ys zs
timestep 1
run 10000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:340)
G vector (1/distance) = 0.25515037
grid = 27 27 72
stencil order = 5
estimated absolute RMS force accuracy = 0.0034946597
estimated relative force accuracy = 1.0524064e-05
using double precision KISS FFT
3d grid and FFT values/proc = 10000 3645
generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 0
2 0.991854 0.602613 8436
2 96.9689 39.7099 2812
Per MPI rank memory allocation (min/avg/max) = 12.75 | 13.98 | 14.61 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 6316.6931 130091.43 1.4011632 415.64004 111.0517 404.90865 0 0 31846.584 -14834.533 -295.4552 -266249.55 -248721.54 8849.777
10000 10000 -289.45045 130091.43 1.4011632 302.33881 40.607755 273.9998 0 0 28985.639 -18356.971 -295.4552 -267593.38 -256650.1 6437.3756
Loop time of 158.311 on 16 procs for 10000 steps with 10468 atoms
Performance: 5.458 ns/day, 4.398 hours/ns, 63.167 timesteps/s
99.1% CPU use with 16 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 30.205 | 89.059 | 116.19 | 363.2 | 56.26
Bond | 0.014853 | 0.050211 | 0.091917 | 9.1 | 0.03
Kspace | 24.485 | 51.722 | 110.71 | 477.6 | 32.67
Neigh | 6.6347 | 6.6473 | 6.6614 | 0.3 | 4.20
Comm | 3.5822 | 4.3034 | 4.61 | 19.4 | 2.72
Output | 0.016708 | 0.018769 | 0.02066 | 0.9 | 0.01
Modify | 5.8045 | 6.0362 | 6.9233 | 15.3 | 3.81
Other | | 0.4745 | | | 0.30
Nlocal: 654.25 ave 775 max 365 min
Histogram: 4 0 0 0 0 0 0 0 2 10
Nghost: 8627.5 ave 10101 max 7261 min
Histogram: 4 0 0 2 2 4 0 0 0 4
Neighs: 320666 ave 418545 max 109066 min
Histogram: 4 0 0 0 0 0 0 1 4 7
Total # of neighbors = 5130655
Ave neighs/atom = 490.12753
Ave special neighs/atom = 1.6709973
Neighbor list builds = 521
Dangerous builds = 0
undump sci
restart 0
dump sci all custom 10000 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) = 0.25515037
grid = 27 27 72
stencil order = 5
estimated absolute RMS force accuracy = 0.0034946597
estimated relative force accuracy = 1.0524064e-05
using double precision KISS FFT
3d grid and FFT values/proc = 10000 3645
generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule
SHAKE stats (type/ave/delta/count) on step 10000
2 0.97 1.18568e-06 8436
2 103.7 9.2964e-05 2812
Per MPI rank memory allocation (min/avg/max) = 13.13 | 14.12 | 14.69 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
10000 10000 -288.85591 130091.43 1.4011632 302.33881 40.607755 273.9998 0 0 28985.639 -18356.971 -295.4552 -267593.38 -256650.1 6437.3756
Loop time of 4.144e-06 on 16 procs for 0 steps with 10468 atoms
122.2% CPU use with 16 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 | | 4.144e-06 | | |100.00
Nlocal: 654.25 ave 775 max 365 min
Histogram: 4 0 0 0 0 0 0 0 2 10
Nghost: 8627.5 ave 10101 max 7261 min
Histogram: 4 0 0 2 2 4 0 0 0 4
Neighs: 320666 ave 418545 max 109066 min
Histogram: 4 0 0 0 0 0 0 1 4 7
Total # of neighbors = 5130655
Ave neighs/atom = 490.12753
Ave special neighs/atom = 1.6709973
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix 4
unfix shaken
log 2.5_NVT.out