#------------------------------------------------------------------------------- # 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 3728 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 2.1655275) to (39.00424 48.916 70.334472) 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 2.1655275) to (39.00424 48.916 70.334472) 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 compute group_1 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_1 all ave/time 1 100 100 c_group_1 file 2.5_GroupInteractions_Layer1_Layer2_1.out timestep 1 run 2000000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0366 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25822755 grid = 32 40 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0031888792 estimated relative force accuracy = 9.6032151e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7429 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule WARNING: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero (../compute_group_group.cpp:140) 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 10 2 neighbor lists, perpetual/occasional/extra = 1 1 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 (2) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none SHAKE stats (type/ave/delta/count) on step 0 2 0.97 2.13148e-09 11184 2 103.7 2.36709e-07 3728 Per MPI rank memory allocation (min/avg/max) = 13.1 | 13.61 | 14.08 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-06 346.45168 130061.67 1.4001311 299.49429 295.56647 375.58239 0 0 34739.812 22310.997 -361.40299 -344972.21 -287250.25 8223.8803 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969971 8.82294e-05 11184 2 103.7 0.00999956 3728 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970052 0.000153379 11184 2 103.7 0.0175874 3728 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970018 5.3828e-05 11184 2 103.7 0.00614528 3728 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969987 4.09767e-05 11184 2 103.7 0.0046507 3728 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969978 6.79129e-05 11184 2 103.7 0.00773146 3728 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970013 3.94859e-05 11184 2 103.7 0.00448154 3728 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970063 0.000187958 11184 2 103.7 0.021579 3728 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970018 5.2611e-05 11184 2 103.7 0.00601997 3728 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970014 4.10892e-05 11184 2 103.7 0.0047123 3728 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969988 3.50653e-05 11184 2 103.7 0.00398872 3728 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970022 6.7276e-05 11184 2 103.7 0.00774018 3728 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970002 6.05806e-06 11184 2 103.7 0.000639836 3728 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970013 3.83676e-05 11184 2 103.7 0.00443078 3728 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970096 0.000283399 11184 2 103.7 0.0324213 3728 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970024 7.15075e-05 11184 2 103.7 0.00823387 3728 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970027 7.97937e-05 11184 2 103.7 0.00919708 3728 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970014 4.02571e-05 11184 2 103.7 0.00463522 3728 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970018 5.36309e-05 11184 2 103.7 0.00609666 3728 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969996 1.37432e-05 11184 2 103.7 0.00151686 3728 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969919 0.000241791 11184 2 103.7 0.0276338 3728 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970041 0.000121313 11184 2 103.7 0.0139193 3728 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970043 0.00012746 11184 2 103.7 0.014613 3728 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970003 9.23039e-06 11184 2 103.7 0.00100027 3728 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969983 5.24768e-05 11184 2 103.7 0.00599097 3728 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.96999 3.14414e-05 11184 2 103.7 0.00354355 3728 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969969 9.27016e-05 11184 2 103.7 0.0105593 3728 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970064 0.00019324 11184 2 103.7 0.0221052 3728 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970046 0.000137133 11184 2 103.7 0.0157669 3728 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970029 8.62181e-05 11184 2 103.7 0.00987738 3728 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969989 3.47944e-05 11184 2 103.7 0.00390871 3728 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969931 0.00020585 11184 2 103.7 0.0235369 3728 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970026 7.77124e-05 11184 2 103.7 0.00893926 3728 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.96999 3.01527e-05 11184 2 103.7 0.00341502 3728 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970021 6.39212e-05 11184 2 103.7 0.00727564 3728 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969996 1.27195e-05 11184 2 103.7 0.00142796 3728 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969954 0.000137283 11184 2 103.7 0.0157267 3728 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97002 5.85963e-05 11184 2 103.7 0.00671524 3728 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970038 0.000114083 11184 2 103.7 0.0130833 3728 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.96995 0.00015187 11184 2 103.7 0.0173178 3728 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969969 9.33376e-05 11184 2 103.7 0.0106633 3728 2000000 2000000 660.1036 131166.15 1.3883414 294.29021 311.62603 343.04031 0 0 35005.977 22110.122 -358.35982 -344952.59 -287181.82 8080.9802 Loop time of 36290.6 on 32 procs for 2000000 steps with 12941 atoms Performance: 4.762 ns/day, 5.040 hours/ns, 55.111 timesteps/s 98.8% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11523 | 13301 | 16605 |1646.2 | 36.65 Bond | 3.2879 | 15.084 | 38.089 | 333.3 | 0.04 Kspace | 4075.7 | 7414.6 | 9226 |2228.4 | 20.43 Neigh | 1310 | 1312 | 1314 | 2.9 | 3.62 Comm | 1194.4 | 1260.9 | 1329.4 | 110.8 | 3.47 Output | 0.014355 | 0.017179 | 0.019799 | 1.3 | 0.00 Modify | 12325 | 12640 | 12898 | 208.3 | 34.83 Other | | 347.1 | | | 0.96 Nlocal: 404.406 ave 477 max 360 min Histogram: 5 7 7 5 0 0 0 0 1 7 Nghost: 8074.25 ave 8310 max 7533 min Histogram: 5 3 0 0 0 0 0 3 5 16 Neighs: 230310 ave 298465 max 189199 min Histogram: 6 6 10 2 0 0 0 0 0 8 Total # of neighbors = 7369934 Ave neighs/atom = 569.50267 Ave special neighs/atom = 2.0236458 Neighbor list builds = 104588 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) = 0.25800955 grid = 32 40 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0032274938 estimated relative force accuracy = 9.7195017e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7429 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule WARNING: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero (../compute_group_group.cpp:140) SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969969 9.33376e-05 11184 2 103.7 0.0106633 3728 Per MPI rank memory allocation (min/avg/max) = 14.63 | 14.91 | 15.6 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 479.33239 131166.15 1.3883414 294.29021 311.62603 343.04031 0 0 35005.977 21821.17 -358.35982 -344663.65 -287181.83 8080.9802 Loop time of 8.29947e-06 on 32 procs for 0 steps with 12941 atoms 102.0% 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 | | 8.299e-06 | | |100.00 Nlocal: 404.406 ave 477 max 360 min Histogram: 5 7 7 5 0 0 0 0 1 7 Nghost: 8074.25 ave 8310 max 7533 min Histogram: 5 3 0 0 0 0 0 3 5 16 Neighs: 230310 ave 298465 max 189199 min Histogram: 6 6 10 2 0 0 0 0 0 8 Total # of neighbors = 7369934 Ave neighs/atom = 569.50267 Ave special neighs/atom = 2.0236458 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_1 unfix group_1 unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 20:47:12