#------------------------------------------------------------------------------- # Stage 2.5: 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 1928 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (40.281352 40.281352 40.281352) 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 (40.281352 40.281352 40.281352) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 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 2.5_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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0171 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25969541 grid = 32 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0026097487 estimated relative force accuracy = 7.8591807e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5175 1024 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 = 6 6 6 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 0.97 5.54778e-13 5784 2 103.7 7.82165e-11 1928 Per MPI rank memory allocation (min/avg/max) = 12.74 | 12.91 | 12.94 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 3288.0363 65360.011 1.3291045 293.94286 25.78052 45.73139 0 0 17366.433 14654.835 -161.84744 -158049.51 -125956.73 3906.0454 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969999 5.53046e-06 5784 2 103.7 0.000578977 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969984 5.00045e-05 5784 2 103.7 0.00568775 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970009 2.7515e-05 5784 2 103.7 0.00312504 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970001 2.69663e-06 5784 2 103.7 0.000302249 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.96994 0.000179413 5784 2 103.7 0.0204867 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969967 9.94356e-05 5784 2 103.7 0.0113354 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970006 1.79173e-05 5784 2 103.7 0.0020394 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969966 0.000104219 5784 2 103.7 0.0119116 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97003 9.05903e-05 5784 2 103.7 0.0103782 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969963 0.000111059 5784 2 103.7 0.0126442 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970013 3.86901e-05 5784 2 103.7 0.00447119 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969978 6.8525e-05 5784 2 103.7 0.00776509 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970019 5.84704e-05 5784 2 103.7 0.00669102 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970041 0.000123105 5784 2 103.7 0.0140183 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970038 0.000116938 5784 2 103.7 0.0133397 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969951 0.000147805 5784 2 103.7 0.0168772 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970044 0.000134334 5784 2 103.7 0.0153386 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970025 7.57832e-05 5784 2 103.7 0.00870319 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969997 1.11299e-05 5784 2 103.7 0.00124376 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969924 0.000230019 5784 2 103.7 0.0263688 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969991 2.67021e-05 5784 2 103.7 0.0030075 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969965 0.000107349 5784 2 103.7 0.0122461 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969982 5.48208e-05 5784 2 103.7 0.00622131 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969975 7.74792e-05 5784 2 103.7 0.00877582 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.96998 5.93607e-05 5784 2 103.7 0.00669163 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970023 6.83704e-05 5784 2 103.7 0.00777369 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970026 7.85531e-05 5784 2 103.7 0.00892734 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970021 6.31112e-05 5784 2 103.7 0.00716143 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969965 0.000106545 5784 2 103.7 0.0121394 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969933 0.000202096 5784 2 103.7 0.0231151 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970021 6.23155e-05 5784 2 103.7 0.00713652 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969976 7.12173e-05 5784 2 103.7 0.00810499 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970043 0.000129585 5784 2 103.7 0.0148377 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.96998 6.07834e-05 5784 2 103.7 0.00694287 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970046 0.000137687 5784 2 103.7 0.0157614 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970012 3.53398e-05 5784 2 103.7 0.00399431 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970001 3.40537e-06 5784 2 103.7 0.000366048 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970013 3.75611e-05 5784 2 103.7 0.00434962 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970071 0.000212506 5784 2 103.7 0.0243187 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970035 0.000103668 5784 2 103.7 0.0118417 1928 2000000 2000000 12.149844 68852.409 1.2616884 302.06575 28.137922 48.540606 0 0 16424.7 15804.85 -153.63806 -158035.43 -125729.2 4013.986 Loop time of 11594.5 on 32 procs for 2000000 steps with 6387 atoms Performance: 14.904 ns/day, 1.610 hours/ns, 172.496 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 | 5812.3 | 6245.8 | 6611.7 | 228.3 | 53.87 Bond | 2.0116 | 4.3754 | 8.6173 | 88.1 | 0.04 Kspace | 2289.9 | 2654 | 3092.7 | 352.8 | 22.89 Neigh | 484.96 | 485.49 | 486.03 | 1.3 | 4.19 Comm | 831.72 | 848.36 | 863.13 | 29.0 | 7.32 Output | 0.0077289 | 0.009574 | 0.011319 | 1.1 | 0.00 Modify | 1214.6 | 1252.8 | 1269.5 | 26.6 | 10.80 Other | | 103.7 | | | 0.89 Nlocal: 199.594 ave 217 max 174 min Histogram: 2 1 0 3 5 4 7 2 4 4 Nghost: 6361.56 ave 6440 max 6302 min Histogram: 4 1 7 5 5 1 4 1 2 2 Neighs: 106333 ave 115959 max 91270 min Histogram: 1 1 2 2 4 4 5 5 3 5 Total # of neighbors = 3402651 Ave neighs/atom = 532.74636 Ave special neighs/atom = 1.8738062 Neighbor list builds = 100292 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.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) = 0.25854065 grid = 32 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0027741828 estimated relative force accuracy = 8.354369e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5175 1024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970035 0.000103668 5784 2 103.7 0.0118417 1928 Per MPI rank memory allocation (min/avg/max) = 12.74 | 12.92 | 12.94 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 213.53098 68852.409 1.2616884 302.06575 28.137922 48.540606 0 0 16424.7 15108.673 -153.63806 -157339.25 -125729.2 4013.986 Loop time of 7.19622e-06 on 32 procs for 0 steps with 6387 atoms 114.6% 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 | | 7.196e-06 | | |100.00 Nlocal: 199.594 ave 217 max 174 min Histogram: 2 1 0 3 5 4 7 2 4 4 Nghost: 6361.56 ave 6440 max 6302 min Histogram: 4 1 7 5 5 1 4 1 2 2 Neighs: 106333 ave 115959 max 91270 min Histogram: 1 1 2 2 4 4 5 5 3 5 Total # of neighbors = 3402651 Ave neighs/atom = 532.74636 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 6:15:27