#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 5 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 2768 = # 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 500000 500000 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 500 1 500 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 5000000 2.4.restart dump sci all custom 500000 2.4.xyz id mol type q xs ys zs timestep 1 run 5000000 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.996848 1.0295 8304 2 96.9475 34.7728 2768 Per MPI rank memory allocation (min/avg/max) = 11.62 | 11.92 | 12.21 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 19049.345 92859.489 1.3074058 428.55654 78.477879 292.28257 0 0 24230.046 -167985.34 -386.0007 0 -143384.53 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.25292e-06 8304 2 103.7 0.00010501 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.5327e-06 8304 2 103.7 0.000109679 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.19632e-06 8304 2 103.7 0.000104991 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.89328e-06 8304 2 103.7 0.000108824 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.44294e-06 8304 2 103.7 0.000116037 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.34099e-06 8304 2 103.7 0.000104411 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.29324e-06 8304 2 103.7 0.000102273 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.58492e-06 8304 2 103.7 0.000105157 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.32451e-06 8304 2 103.7 8.82637e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.22917e-06 8304 2 103.7 0.000102355 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.3174e-06 8304 2 103.7 0.00010504 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.60012e-06 8304 2 103.7 9.96995e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.48105e-06 8304 2 103.7 0.000101217 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.42099e-06 8304 2 103.7 9.64227e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.36503e-06 8304 2 103.7 0.000102295 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.4376e-06 8304 2 103.7 0.000108372 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.36696e-06 8304 2 103.7 9.66753e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.40465e-06 8304 2 103.7 9.75148e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.6659e-06 8304 2 103.7 0.00010661 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.47682e-06 8304 2 103.7 9.55233e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.89634e-06 8304 2 103.7 0.000106368 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.27036e-06 8304 2 103.7 9.51056e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.36014e-06 8304 2 103.7 0.000102793 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.63328e-06 8304 2 103.7 0.000108101 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.5457e-06 8304 2 103.7 0.000104925 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.34368e-06 8304 2 103.7 0.000118373 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.45497e-06 8304 2 103.7 0.000102361 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.53498e-06 8304 2 103.7 0.000128343 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.45659e-06 8304 2 103.7 0.000103696 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.41299e-06 8304 2 103.7 0.000100132 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.70229e-06 8304 2 103.7 0.000119677 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.62891e-06 8304 2 103.7 0.00010283 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.23583e-06 8304 2 103.7 9.18155e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.38868e-06 8304 2 103.7 0.000119411 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.42659e-06 8304 2 103.7 0.000100118 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.32172e-06 8304 2 103.7 9.20116e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.44795e-06 8304 2 103.7 0.000128436 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.17988e-06 8304 2 103.7 9.66358e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.31293e-06 8304 2 103.7 0.00011642 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.35993e-06 8304 2 103.7 0.000108411 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.56665e-06 8304 2 103.7 9.95829e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.81114e-06 8304 2 103.7 0.000114998 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.28326e-06 8304 2 103.7 9.34076e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.36701e-06 8304 2 103.7 0.000115549 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.50928e-06 8304 2 103.7 0.000104144 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.84898e-06 8304 2 103.7 0.000104227 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.55365e-06 8304 2 103.7 9.98992e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.8798e-06 8304 2 103.7 0.000102576 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.43059e-06 8304 2 103.7 0.000111601 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.31063e-06 8304 2 103.7 0.000106517 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.61275e-06 8304 2 103.7 9.90375e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.30809e-06 8304 2 103.7 9.37444e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.20295e-06 8304 2 103.7 0.00010046 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.73954e-06 8304 2 103.7 0.000110488 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.27694e-06 8304 2 103.7 9.94632e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.64363e-06 8304 2 103.7 0.000112014 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.60208e-06 8304 2 103.7 0.000102035 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.36905e-06 8304 2 103.7 0.000103751 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 2.07906e-06 8304 2 103.7 0.000120663 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.46041e-06 8304 2 103.7 0.000140982 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.72319e-06 8304 2 103.7 0.000118205 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.97998e-06 8304 2 103.7 0.000106083 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.38656e-06 8304 2 103.7 0.000104243 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.73775e-06 8304 2 103.7 0.000122559 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.61338e-06 8304 2 103.7 0.000115559 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.49233e-06 8304 2 103.7 0.000113048 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.50253e-06 8304 2 103.7 0.000115676 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.7671e-06 8304 2 103.7 0.000114823 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.40433e-06 8304 2 103.7 0.000106776 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.92675e-06 8304 2 103.7 0.000131776 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.30414e-06 8304 2 103.7 9.70935e-05 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.47281e-06 8304 2 103.7 9.32147e-05 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.64685e-06 8304 2 103.7 0.000105991 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.43293e-06 8304 2 103.7 9.91898e-05 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.58832e-06 8304 2 103.7 0.000102161 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.32636e-06 8304 2 103.7 0.000102222 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.43995e-06 8304 2 103.7 9.63271e-05 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 2.04014e-06 8304 2 103.7 0.000134756 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.42521e-06 8304 2 103.7 0.00010008 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.47912e-06 8304 2 103.7 0.000112053 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.71218e-06 8304 2 103.7 0.00011115 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.33586e-06 8304 2 103.7 9.38313e-05 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.5772e-06 8304 2 103.7 9.72371e-05 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.20678e-06 8304 2 103.7 0.000117817 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.31737e-06 8304 2 103.7 0.000102834 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.30529e-06 8304 2 103.7 9.46738e-05 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.6259e-06 8304 2 103.7 0.000100937 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.26017e-06 8304 2 103.7 0.000103521 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.39131e-06 8304 2 103.7 0.000114648 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.58256e-06 8304 2 103.7 0.000100772 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.74572e-06 8304 2 103.7 0.00012325 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.20304e-06 8304 2 103.7 9.34515e-05 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.37018e-06 8304 2 103.7 0.000117988 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.47328e-06 8304 2 103.7 9.68365e-05 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.15488e-06 8304 2 103.7 0.000100495 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.15066e-06 8304 2 103.7 9.61397e-05 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.34825e-06 8304 2 103.7 0.000113003 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.30816e-06 8304 2 103.7 9.98799e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.69389e-06 8304 2 103.7 0.000112702 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.83572e-06 8304 2 103.7 0.000102331 2768 5000000 5000000 188.04467 92859.489 1.3074058 302.64407 46.110376 113.18707 0 0 21681.82 -180946.69 -386.0007 0 -159105.58 5712.2523 Loop time of 16851 on 32 procs for 5000000 steps with 9101 atoms Performance: 25.636 ns/day, 0.936 hours/ns, 296.719 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 | 11231 | 12564 | 14227 | 677.1 | 74.56 Bond | 3.9769 | 9.9095 | 17.238 | 123.5 | 0.06 Neigh | 811.33 | 813.74 | 815.76 | 3.8 | 4.83 Comm | 599.03 | 2058.9 | 3547.1 |1605.3 | 12.22 Output | 0.010044 | 0.012302 | 0.014471 | 1.2 | 0.00 Modify | 1071.8 | 1342.6 | 1831.9 | 633.2 | 7.97 Other | | 61.52 | | | 0.37 Nlocal: 284.406 ave 306 max 257 min Histogram: 2 1 2 3 2 6 6 5 3 2 Nghost: 5370.88 ave 5494 max 5228 min Histogram: 1 2 4 4 3 4 5 2 4 3 Neighs: 100418 ave 113214 max 86521 min Histogram: 3 0 2 4 5 6 4 5 2 1 Total # of neighbors = 3213375 Ave neighs/atom = 353.07933 Ave special neighs/atom = 1.8929788 Neighbor list builds = 238708 Dangerous builds = 1 undump sci restart 0 dump sci all custom 5000000 2.4.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.83572e-06 8304 2 103.7 0.000102331 2768 Per MPI rank memory allocation (min/avg/max) = 11.63 | 12.05 | 12.21 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 5000000 5000000 189.08254 92859.489 1.3074058 302.64407 46.110376 113.18707 0 0 21681.82 -180946.69 -386.0007 0 -159105.58 5712.2523 Loop time of 7.63441e-06 on 32 procs for 0 steps with 9101 atoms 104.8% 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 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 | | 7.634e-06 | | |100.00 Nlocal: 284.406 ave 306 max 257 min Histogram: 2 1 2 3 2 6 6 5 3 2 Nghost: 5370.88 ave 5494 max 5228 min Histogram: 1 2 4 4 3 4 5 2 4 3 Neighs: 100418 ave 113214 max 86521 min Histogram: 3 0 2 4 5 6 4 5 2 1 Total # of neighbors = 3213375 Ave neighs/atom = 353.07933 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out