#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 10 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 1000 1000 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 1 1 1 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 10000 2.5.restart dump sci all custom 1000 2.5.xyz id mol type q xs ys zs group rdfgroup_1 union subset_Li_1 subset_Cl_1 350 atoms in group rdfgroup_1 compute rdf_1 rdfgroup_1 rdf 200 4 1 fix rdf_1 rdfgroup_1 ave/time 1 100 100 c_rdf_1[*] file 2.5_PairCorrelation_all_1.out mode vector group rdfgroup_2 union subset_Li_1 subset_S_1 38 atoms in group rdfgroup_2 compute rdf_2 rdfgroup_2 rdf 200 4 9 fix rdf_2 rdfgroup_2 ave/time 1 100 100 c_rdf_2[*] file 2.5_PairCorrelation_all_2.out mode vector group rdfgroup_3 union subset_Li_1 subset_O(SO4)_1 38 atoms in group rdfgroup_3 compute rdf_3 rdfgroup_3 rdf 200 4 8 fix rdf_3 rdfgroup_3 ave/time 1 100 100 c_rdf_3[*] file 2.5_PairCorrelation_all_3.out mode vector group rdfgroup_4 union subset_Li_1 subset_O(H2O)_1 2819 atoms in group rdfgroup_4 compute rdf_4 rdfgroup_4 rdf 200 4 7 fix rdf_4 rdfgroup_4 ave/time 1 100 100 c_rdf_4[*] file 2.5_PairCorrelation_all_4.out mode vector group rdfgroup_5 union subset_Li_1 subset_H_1 2819 atoms in group rdfgroup_5 compute rdf_5 rdfgroup_5 rdf 200 4 2 fix rdf_5 rdfgroup_5 ave/time 1 100 100 c_rdf_5[*] file 2.5_PairCorrelation_all_5.out mode vector group rdfgroup_6 union subset_Na_1 subset_Cl_1 399 atoms in group rdfgroup_6 compute rdf_6 rdfgroup_6 rdf 200 6 1 fix rdf_6 rdfgroup_6 ave/time 1 100 100 c_rdf_6[*] file 2.5_PairCorrelation_all_6.out mode vector group rdfgroup_8 union subset_Na_1 subset_S_1 87 atoms in group rdfgroup_8 compute rdf_8 rdfgroup_8 rdf 200 6 9 fix rdf_8 rdfgroup_8 ave/time 1 100 100 c_rdf_8[*] file 2.5_PairCorrelation_all_8.out mode vector group rdfgroup_9 union subset_Na_1 subset_O(SO4)_1 87 atoms in group rdfgroup_9 compute rdf_9 rdfgroup_9 rdf 200 6 8 fix rdf_9 rdfgroup_9 ave/time 1 100 100 c_rdf_9[*] file 2.5_PairCorrelation_all_9.out mode vector group rdfgroup_10 union subset_Na_1 subset_O(H2O)_1 2868 atoms in group rdfgroup_10 compute rdf_10 rdfgroup_10 rdf 200 6 7 fix rdf_10 rdfgroup_10 ave/time 1 100 100 c_rdf_10[*] file 2.5_PairCorrelation_all_10.out mode vector group rdfgroup_11 union subset_Na_1 subset_H_1 2868 atoms in group rdfgroup_11 compute rdf_11 rdfgroup_11 rdf 200 6 2 fix rdf_11 rdfgroup_11 ave/time 1 100 100 c_rdf_11[*] file 2.5_PairCorrelation_all_11.out mode vector group rdfgroup_12 union subset_K_1 subset_Cl_1 383 atoms in group rdfgroup_12 compute rdf_12 rdfgroup_12 rdf 200 3 1 fix rdf_12 rdfgroup_12 ave/time 1 100 100 c_rdf_12[*] file 2.5_PairCorrelation_all_12.out mode vector group rdfgroup_13 union subset_K_1 subset_S_1 71 atoms in group rdfgroup_13 compute rdf_13 rdfgroup_13 rdf 200 3 9 fix rdf_13 rdfgroup_13 ave/time 1 100 100 c_rdf_13[*] file 2.5_PairCorrelation_all_13.out mode vector group rdfgroup_14 union subset_K_1 subset_O(SO4)_1 71 atoms in group rdfgroup_14 compute rdf_14 rdfgroup_14 rdf 200 3 8 fix rdf_14 rdfgroup_14 ave/time 1 100 100 c_rdf_14[*] file 2.5_PairCorrelation_all_14.out mode vector group rdfgroup_15 union subset_K_1 subset_O(H2O)_1 2852 atoms in group rdfgroup_15 compute rdf_15 rdfgroup_15 rdf 200 3 7 fix rdf_15 rdfgroup_15 ave/time 1 100 100 c_rdf_15[*] file 2.5_PairCorrelation_all_15.out mode vector group rdfgroup_16 union subset_K_1 subset_H_1 2852 atoms in group rdfgroup_16 compute rdf_16 rdfgroup_16 rdf 200 3 2 fix rdf_16 rdfgroup_16 ave/time 1 100 100 c_rdf_16[*] file 2.5_PairCorrelation_all_16.out mode vector compute group_22 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_22 all ave/time 1 100 100 c_group_22 file 2.5_GroupInteractions_Layer1_Layer2_22.out compute group_23 subset_Layer1 group/group subset_Layer2 pair yes kspace no 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 no kspace yes fix group_24 all ave/time 1 100 100 c_group_24 file 2.5_GroupInteractions_Layer1_Layer2_24.out timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25515037 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034946597 estimated relative force accuracy = 1.0524064e-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 18 neighbor lists, perpetual/occasional/extra = 1 17 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 rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (5) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (6) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (7) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (8) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (9) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (10) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (11) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (12) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (13) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (14) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (15) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (16) compute rdf, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (17) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (18) 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 7.05436e-13 8436 2 103.7 7.75913e-11 2812 Per MPI rank memory allocation (min/avg/max) = 13.13 | 14.08 | 14.67 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 -288.85079 130091.43 1.4011632 302.33881 40.607755 273.9998 0 0 28985.638 -18356.95 -295.4552 -267593.38 -256650.08 6437.3756 10000 10000 -117.39709 130091.43 1.4011632 302.46578 43.262466 270.24002 0 0 29239.249 -18838.223 -295.4552 -267593.1 -256878.58 6440.0792 Loop time of 303.098 on 16 procs for 10000 steps with 10468 atoms Performance: 2.851 ns/day, 8.419 hours/ns, 32.993 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 | 30.29 | 88.308 | 117.44 | 355.1 | 29.14 Bond | 0.019459 | 0.055615 | 0.11846 | 10.2 | 0.02 Kspace | 23.042 | 52.162 | 110.34 | 463.5 | 17.21 Neigh | 6.4282 | 6.4403 | 6.4553 | 0.3 | 2.12 Comm | 3.9419 | 4.7226 | 5.1072 | 20.0 | 1.56 Output | 0.016821 | 0.018838 | 0.020783 | 0.9 | 0.01 Modify | 150.68 | 150.89 | 151.45 | 2.6 | 49.78 Other | | 0.499 | | | 0.16 Nlocal: 654.25 ave 775 max 372 min Histogram: 4 0 0 0 0 0 0 0 3 9 Nghost: 8607.19 ave 10076 max 7244 min Histogram: 4 0 0 2 2 4 0 0 0 4 Neighs: 320385 ave 415975 max 110871 min Histogram: 4 0 0 0 0 0 0 2 3 7 Total # of neighbors = 5126164 Ave neighs/atom = 489.69851 Ave special neighs/atom = 1.6709973 Neighbor list builds = 502 Dangerous builds = 0 undump sci restart 0 dump sci all custom 10000 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) = 0.25515037 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034946597 estimated relative force accuracy = 1.0524064e-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 10000 2 0.97 1.58328e-06 8436 2 103.7 0.000120747 2812 Per MPI rank memory allocation (min/avg/max) = 26.1 | 40.06 | 47.12 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 10000 10000 -116.90035 130091.43 1.4011632 302.46578 43.262466 270.24002 0 0 29239.249 -18838.223 -295.4552 -267593.1 -256878.58 6440.0792 Loop time of 4.41194e-06 on 16 procs for 0 steps with 10468 atoms 126.1% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 4.412e-06 | | |100.00 Nlocal: 654.25 ave 775 max 372 min Histogram: 4 0 0 0 0 0 0 0 3 9 Nghost: 8607.19 ave 10076 max 7244 min Histogram: 4 0 0 2 2 4 0 0 0 4 Neighs: 320385 ave 415975 max 110871 min Histogram: 4 0 0 0 0 0 0 2 3 7 Total # of neighbors = 5126164 Ave neighs/atom = 489.69851 Ave special neighs/atom = 1.6709973 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_1 unfix rdf_1 group rdfgroup_1 delete uncompute rdf_2 unfix rdf_2 group rdfgroup_2 delete uncompute rdf_3 unfix rdf_3 group rdfgroup_3 delete uncompute rdf_4 unfix rdf_4 group rdfgroup_4 delete uncompute rdf_5 unfix rdf_5 group rdfgroup_5 delete uncompute rdf_6 unfix rdf_6 group rdfgroup_6 delete uncompute rdf_8 unfix rdf_8 group rdfgroup_8 delete uncompute rdf_9 unfix rdf_9 group rdfgroup_9 delete uncompute rdf_10 unfix rdf_10 group rdfgroup_10 delete uncompute rdf_11 unfix rdf_11 group rdfgroup_11 delete uncompute rdf_12 unfix rdf_12 group rdfgroup_12 delete uncompute rdf_13 unfix rdf_13 group rdfgroup_13 delete uncompute rdf_14 unfix rdf_14 group rdfgroup_14 delete uncompute rdf_15 unfix rdf_15 group rdfgroup_15 delete uncompute rdf_16 unfix rdf_16 group rdfgroup_16 delete uncompute group_22 unfix group_22 uncompute group_23 unfix group_23 uncompute group_24 unfix group_24 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 0:07:46