#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 200 ps 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 2812 = # 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 20000 20000 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 2.5_averages.txt off 1 fix 3 movable ave/time 20 1 20 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 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 200000 2.5.restart dump sci all custom 20000 2.5.xyz id mol type q xs ys zs group rdfgroup_2 union subset_Li_1 subset_Li_1 7 atoms in group rdfgroup_2 compute rdf_2 rdfgroup_2 rdf 200 4 4 fix rdf_2 rdfgroup_2 ave/time 1 200000 200000 c_rdf_2[*] file 2.5_PairCorrelation_all_2.out mode vector group rdfgroup_3 union subset_Li_1 subset_Cl_1 350 atoms in group rdfgroup_3 compute rdf_3 rdfgroup_3 rdf 200 4 1 fix rdf_3 rdfgroup_3 ave/time 1 200000 200000 c_rdf_3[*] file 2.5_PairCorrelation_all_3.out mode vector compute group_23 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_23 all ave/time 1 100 100 c_group_23 file 2.5_GroupInteractions_Layer1_Layer2_23.out compute group_24 subset_Layer1 group/group subset_Layer2 pair yes kspace no fix group_24 all ave/time 1 100 100 c_group_24 file 2.5_GroupInteractions_Layer1_Layer2_24.out compute group_25 subset_Layer1 group/group subset_Layer2 pair no kspace yes fix group_25 all ave/time 1 100 100 c_group_25 file 2.5_GroupInteractions_Layer1_Layer2_25.out timestep 1 run 200000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25531922 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034643513 estimated relative force accuracy = 1.0432791e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3645 generated 0 of 36 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 = 5 5 18 5 neighbor lists, perpetual/occasional/extra = 1 4 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard (2) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (3) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (4) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (5) 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 6.9611e-13 8436 2 103.7 7.70513e-11 2812 Per MPI rank memory allocation (min/avg/max) = 13.13 | 14.18 | 14.71 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-06 945.15857 129126.99 1.4116283 297.75324 39.120193 76.638149 0 0 29832.547 -19506.619 -297.66192 -267778.09 -257336.4 6339.74 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.36714e-06 8436 2 103.7 0.00010657 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.26902e-06 8436 2 103.7 9.23808e-05 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.39795e-06 8436 2 103.7 9.48403e-05 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.25017e-06 8436 2 103.7 9.61429e-05 2812 200000 200000 944.82543 129126.99 1.4116283 295.89622 39.180969 71.112714 0 0 29905.494 -19425.94 -297.66192 -267786.69 -257196.84 6300.2005 Loop time of 4754.72 on 16 procs for 200000 steps with 10468 atoms Performance: 3.634 ns/day, 6.604 hours/ns, 42.063 timesteps/s 99.1% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 612.6 | 1742 | 2238 |1577.7 | 36.64 Bond | 0.32001 | 0.93932 | 1.7383 | 41.0 | 0.02 Kspace | 474.86 | 973.54 | 2106.1 |2117.0 | 20.48 Neigh | 123.44 | 123.65 | 123.89 | 1.4 | 2.60 Comm | 78.177 | 93.44 | 100.47 | 88.6 | 1.97 Output | 0.016686 | 0.018786 | 0.020759 | 0.9 | 0.00 Modify | 1808.5 | 1812.8 | 1823.9 | 14.8 | 38.13 Other | | 8.319 | | | 0.17 Nlocal: 654.25 ave 799 max 364 min Histogram: 4 0 0 0 0 0 0 0 8 4 Nghost: 8654.12 ave 10085 max 7344 min Histogram: 4 0 0 2 2 4 0 0 0 4 Neighs: 322880 ave 435963 max 108664 min Histogram: 4 0 0 0 0 0 0 4 2 6 Total # of neighbors = 5166082 Ave neighs/atom = 493.51185 Ave special neighs/atom = 1.6709973 Neighbor list builds = 9916 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 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) = 0.25531922 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034643513 estimated relative force accuracy = 1.0432791e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3645 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.25017e-06 8436 2 103.7 9.61429e-05 2812 Per MPI rank memory allocation (min/avg/max) = 16.18 | 20.42 | 22.35 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 200000 200000 945.40494 129126.99 1.4116283 295.89622 39.180969 71.112714 0 0 29905.494 -19425.94 -297.66192 -267786.69 -257196.84 6300.2005 Loop time of 4.57456e-06 on 16 procs for 0 steps with 10468 atoms 117.5% CPU use with 16 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 | | 4.575e-06 | | |100.00 Nlocal: 654.25 ave 799 max 364 min Histogram: 4 0 0 0 0 0 0 0 8 4 Nghost: 8654.12 ave 10085 max 7344 min Histogram: 4 0 0 2 2 4 0 0 0 4 Neighs: 322880 ave 435963 max 108664 min Histogram: 4 0 0 0 0 0 0 4 2 6 Total # of neighbors = 5166082 Ave neighs/atom = 493.51185 Ave special neighs/atom = 1.6709973 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_2 unfix rdf_2 group rdfgroup_2 delete uncompute rdf_3 unfix rdf_3 group rdfgroup_3 delete uncompute group_23 unfix group_23 uncompute group_24 unfix group_24 uncompute group_25 unfix group_25 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 2:10:10