#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 ns 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 1928 = # 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 200000 200000 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 200 1 200 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 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) = 0.25584802 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0034810988 estimated relative force accuracy = 1.0483226e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4312 960 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00309 0.106049 5784 2 97.0092 12.6126 1928 Per MPI rank memory allocation (min/avg/max) = 12.67 | 12.81 | 12.87 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 2453.6078 65360.011 1.3291045 427.16581 6.4849146 59.28801 0 0 20420.872 758.96221 -161.84744 -155722.75 -134477.14 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.30365e-06 5784 2 103.7 0.000107339 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.34141e-06 5784 2 103.7 0.000113678 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.0657e-06 5784 2 103.7 8.46672e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.27891e-06 5784 2 103.7 8.63612e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.16266e-06 5784 2 103.7 0.000102159 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.17026e-06 5784 2 103.7 0.00010308 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.1853e-06 5784 2 103.7 8.85763e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.2957e-06 5784 2 103.7 9.59806e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.32179e-06 5784 2 103.7 0.00010445 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.264e-06 5784 2 103.7 0.000103775 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.19783e-06 5784 2 103.7 9.28883e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.45375e-06 5784 2 103.7 0.000105452 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.13114e-06 5784 2 103.7 8.75374e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.14777e-06 5784 2 103.7 8.74219e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.65794e-06 5784 2 103.7 0.000151651 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.21202e-06 5784 2 103.7 9.58126e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.3182e-06 5784 2 103.7 0.000105942 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.26424e-06 5784 2 103.7 8.91367e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.40269e-06 5784 2 103.7 0.000115649 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.25759e-06 5784 2 103.7 0.000130579 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.28856e-06 5784 2 103.7 9.10224e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.15223e-06 5784 2 103.7 9.03885e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.21035e-06 5784 2 103.7 9.57836e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.25588e-06 5784 2 103.7 9.89675e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.43817e-06 5784 2 103.7 9.9723e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.79432e-06 5784 2 103.7 0.000147702 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.19527e-06 5784 2 103.7 9.97151e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.11673e-06 5784 2 103.7 8.94588e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.79773e-06 5784 2 103.7 0.000103947 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.06997e-06 5784 2 103.7 8.7524e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.35257e-06 5784 2 103.7 0.000103654 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.15196e-06 5784 2 103.7 9.89318e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.04169e-06 5784 2 103.7 0.000102604 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.54245e-06 5784 2 103.7 0.000109003 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.55923e-06 5784 2 103.7 9.93927e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.10615e-06 5784 2 103.7 8.78357e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.52074e-06 5784 2 103.7 0.000103357 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.3318e-06 5784 2 103.7 0.000110501 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.09092e-06 5784 2 103.7 8.86798e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.09103e-06 5784 2 103.7 9.0064e-05 1928 2000000 2000000 3604.0609 65360.011 1.3291045 298.96649 31.496455 34.335384 0 0 17482.918 12152.161 -161.84744 -155726.15 -126025.24 3972.8016 Loop time of 10820.3 on 32 procs for 2000000 steps with 6387 atoms Performance: 15.970 ns/day, 1.503 hours/ns, 184.838 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 | 5765.4 | 6425.5 | 6935.7 | 381.0 | 59.38 Bond | 2.0078 | 4.2112 | 6.7748 | 71.0 | 0.04 Kspace | 1894.2 | 2410.9 | 3072.2 | 623.4 | 22.28 Neigh | 361.52 | 361.87 | 362.36 | 1.1 | 3.34 Comm | 838.79 | 851.47 | 864.91 | 22.1 | 7.87 Output | 0.010583 | 0.012475 | 0.01428 | 1.0 | 0.00 Modify | 724.18 | 731.34 | 739.7 | 14.7 | 6.76 Other | | 34.94 | | | 0.32 Nlocal: 199.594 ave 216 max 180 min Histogram: 2 1 4 2 2 8 3 4 3 3 Nghost: 6600.34 ave 6646 max 6542 min Histogram: 1 1 2 3 6 6 5 2 4 2 Neighs: 112036 ave 127073 max 94128 min Histogram: 1 2 1 2 9 6 2 6 2 1 Total # of neighbors = 3585144 Ave neighs/atom = 561.31893 Ave special neighs/atom = 1.8738062 Neighbor list builds = 94867 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) = 0.25584802 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0034810988 estimated relative force accuracy = 1.0483226e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4312 960 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.09103e-06 5784 2 103.7 9.0064e-05 1928 Per MPI rank memory allocation (min/avg/max) = 12.67 | 12.84 | 12.87 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 3605.1002 65360.011 1.3291045 298.96649 31.496455 34.335384 0 0 17482.918 12152.161 -161.84744 -155726.15 -126025.24 3972.8016 Loop time of 1.03343e-05 on 32 procs for 0 steps with 6387 atoms 130.6% 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 | | 1.033e-05 | | |100.00 Nlocal: 199.594 ave 216 max 180 min Histogram: 2 1 4 2 2 8 3 4 3 3 Nghost: 6600.34 ave 6646 max 6542 min Histogram: 1 1 2 3 6 6 5 2 4 2 Neighs: 112036 ave 127073 max 94128 min Histogram: 1 2 1 2 9 6 2 6 2 1 Total # of neighbors = 3585144 Ave neighs/atom = 561.31893 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out