#------------------------------------------------------------------------------- # 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3968 = # 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 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_1 403 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(SO4)_1 41 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)_1 134 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 2778 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(H2O)_1 5546 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_1 395 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(SO4)_1 33 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)_1 126 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 2770 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(H2O)_1 5538 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_1 424 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(SO4)_1 62 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)_1 155 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 2799 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(H2O)_1 5567 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) = 0.26029305 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845304 estimated relative force accuracy = 8.3855307e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 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) 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 = 5 7 13 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 1 0.97 6.81122e-13 11904 2 103.7 8.05329e-11 3968 Per MPI rank memory allocation (min/avg/max) = 14.87 | 15.13 | 15.85 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-06 584.36649 139006.3 1.4192018 294.9225 342.91782 661.85005 0 0 37842.735 23526.794 -396.67289 -380001.28 -317626.99 8731.3002 10000 10000 -129.62892 139006.3 1.4192018 300.01595 341.90693 669.38042 0 0 37581.563 23272.293 -396.67289 -380014.82 -318149.67 8882.094 Loop time of 472.349 on 16 procs for 10000 steps with 13901 atoms Performance: 1.829 ns/day, 13.121 hours/ns, 21.171 timesteps/s 98.8% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 109.63 | 133.82 | 172.55 | 186.8 | 28.33 Bond | 0.061757 | 0.16888 | 0.38447 | 29.5 | 0.04 Kspace | 28.759 | 67.768 | 92.122 | 264.4 | 14.35 Neigh | 9.382 | 9.391 | 9.4008 | 0.2 | 1.99 Comm | 4.5435 | 4.7246 | 4.9054 | 5.4 | 1.00 Output | 0.0211 | 0.023533 | 0.0259 | 1.0 | 0.00 Modify | 255.74 | 255.85 | 255.95 | 0.5 | 54.16 Other | | 0.6033 | | | 0.13 Nlocal: 868.812 ave 1009 max 786 min Histogram: 4 3 2 3 0 0 0 0 1 3 Nghost: 10627 ave 11149 max 9879 min Histogram: 4 0 0 0 0 3 1 4 0 4 Neighs: 502483 ave 652730 max 413644 min Histogram: 4 2 6 0 0 0 0 0 0 4 Total # of neighbors = 8039733 Ave neighs/atom = 578.35645 Ave special neighs/atom = 2.0450327 Neighbor list builds = 516 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) = 0.26029305 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845304 estimated relative force accuracy = 8.3855307e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 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) 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 10000 1 0.97 1.24227e-06 11904 2 103.7 8.57533e-05 3968 Per MPI rank memory allocation (min/avg/max) = 47.3 | 51.66 | 61.25 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 -128.47313 139006.3 1.4192018 300.01595 341.90693 669.38042 0 0 37581.563 23272.293 -396.67289 -380014.82 -318149.67 8882.094 Loop time of 4.14444e-06 on 16 procs for 0 steps with 13901 atoms 128.2% 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 | | 4.144e-06 | | |100.00 Nlocal: 868.812 ave 1009 max 786 min Histogram: 4 3 2 3 0 0 0 0 1 3 Nghost: 10627 ave 11149 max 9879 min Histogram: 4 0 0 0 0 3 1 4 0 4 Neighs: 502483 ave 652730 max 413644 min Histogram: 4 2 6 0 0 0 0 0 0 4 Total # of neighbors = 8039733 Ave neighs/atom = 578.35645 Ave special neighs/atom = 2.0450327 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 shaken Total wall time: 0:11:43