#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 960 = # of frozen angles find clusters CPU = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (39.00424 48.916 19.5) 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 (39.00424 48.916 19.5) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 x 1 1 100 y 1 1 100 z 1 1 100 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 ... WARNING: System is not charge neutral, net charge = 0.016 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2632259 grid = 32 36 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0027916347 estimated relative force accuracy = 8.406925e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4080 800 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 7 3 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 2 1.0205 0.0834045 2880 2 97.2385 9.24794 960 Per MPI rank memory allocation (min/avg/max) = 12.07 | 12.07 | 12.08 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 1983.4223 37204.662 1.6314719 397.63453 45.7111 214.21525 0 0 15684.565 -17265.717 -139.55284 -130723.88 -132045.1 3412.4009 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969996 0.000353618 2880 2 103.701 0.0390417 960 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969973 0.000109907 2880 2 103.7 0.0126873 960 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97004 0.00035603 2880 2 103.702 0.0372107 960 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970003 0.000343119 2880 2 103.701 0.0366009 960 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969976 8.81825e-05 2880 2 103.7 0.0099562 960 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970009 0.000515286 2880 2 103.698 0.0542288 960 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969927 0.000361076 2880 2 103.7 0.0398668 960 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970057 0.000128566 2880 2 103.7 0.0144196 960 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969946 6.98356e-05 2880 2 103.7 0.00737874 960 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969999 0.000301238 2880 2 103.698 0.0331963 960 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970063 0.000144109 2880 2 103.699 0.016288 960 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969883 0.000275688 2880 2 103.7 0.0312159 960 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969994 0.000276527 2880 2 103.699 0.0304371 960 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970029 0.000282122 2880 2 103.699 0.0314201 960 SHAKE stats (type/ave/delta/count) on step 750000 2 0.96998 0.000166841 2880 2 103.699 0.0184641 960 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970095 0.000150194 2880 2 103.7 0.0168623 960 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969987 0.000371802 2880 2 103.698 0.0387793 960 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970042 0.000256201 2880 2 103.701 0.0278874 960 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970092 0.00040263 2880 2 103.701 0.0459694 960 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969975 0.000570303 2880 2 103.699 0.0644827 960 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970075 0.000147628 2880 2 103.7 0.0165677 960 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970068 0.000284997 2880 2 103.7 0.032245 960 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969949 0.000142619 2880 2 103.701 0.015654 960 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969974 0.000205385 2880 2 103.701 0.023331 960 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970119 0.000230059 2880 2 103.7 0.0257952 960 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970062 0.000374119 2880 2 103.699 0.0420871 960 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969896 0.000135735 2880 2 103.699 0.0152515 960 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969993 0.000209908 2880 2 103.699 0.0232773 960 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969921 0.000501275 2880 2 103.7 0.0571826 960 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969992 5.44492e-05 2880 2 103.7 0.00613643 960 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970039 0.000343097 2880 2 103.701 0.0389612 960 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970012 0.00043845 2880 2 103.698 0.0484996 960 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969864 0.000442381 2880 2 103.698 0.0468566 960 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970157 0.000210304 2880 2 103.699 0.023608 960 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97001 0.000193617 2880 2 103.699 0.0205108 960 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969895 0.000278382 2880 2 103.7 0.0315066 960 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.96991 0.000227315 2880 2 103.699 0.0263534 960 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970014 0.000102065 2880 2 103.7 0.0114613 960 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969974 0.000368454 2880 2 103.699 0.0422632 960 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969961 0.000373675 2880 2 103.698 0.0399128 960 2000000 2000000 933.18167 33873.415 1.7919174 296.19128 267.98997 326.08558 0 0 13090.758 -8277.6998 -153.27703 -130742.68 -125335.54 2541.8402 Loop time of 8448.68 on 32 procs for 2000000 steps with 3840 atoms Performance: 20.453 ns/day, 1.173 hours/ns, 236.723 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4249.3 | 4522.2 | 4674.4 | 153.3 | 53.53 Bond | 10.218 | 11.548 | 12.893 | 18.7 | 0.14 Kspace | 1560.7 | 1708 | 1975.1 | 251.5 | 20.22 Neigh | 295.48 | 295.82 | 296.59 | 1.7 | 3.50 Comm | 782.84 | 790.65 | 803.2 | 20.0 | 9.36 Output | 0.0063347 | 0.0077849 | 0.0091475 | 1.0 | 0.00 Modify | 997.55 | 1034 | 1067.3 | 92.7 | 12.24 Other | | 86.56 | | | 1.02 Nlocal: 120 ave 126 max 110 min Histogram: 2 0 2 3 2 2 5 7 7 2 Nghost: 6257.59 ave 6302 max 6192 min Histogram: 2 1 1 2 5 4 6 2 6 3 Neighs: 78099.3 ave 81834 max 70824 min Histogram: 2 0 1 3 2 2 4 7 7 4 Total # of neighbors = 2499177 Ave neighs/atom = 650.82734 Ave special neighs/atom = 2.3333333 Neighbor list builds = 86880 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) = 0.26459782 grid = 27 36 24 stencil order = 5 estimated absolute RMS force accuracy = 0.0026336514 estimated relative force accuracy = 7.9311631e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4256 810 generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969961 0.000373675 2880 2 103.698 0.0399128 960 Per MPI rank memory allocation (min/avg/max) = 12.07 | 12.09 | 12.28 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 700.58624 33873.415 1.7919174 296.19128 267.98997 326.08558 0 0 13090.758 -7601.4348 -153.27703 -131418.95 -125335.55 2541.8402 Loop time of 6.58103e-06 on 32 procs for 0 steps with 3840 atoms 120.1% 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 | | 6.581e-06 | | |100.00 Nlocal: 120 ave 126 max 110 min Histogram: 2 0 2 3 2 2 5 7 7 2 Nghost: 6257.59 ave 6302 max 6192 min Histogram: 2 1 1 2 5 4 6 2 6 3 Neighs: 78099.3 ave 81834 max 70824 min Histogram: 2 0 1 3 2 2 4 7 7 4 Total # of neighbors = 2499177 Ave neighs/atom = 650.82734 Ave special neighs/atom = 2.3333333 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 2:20:53