#------------------------------------------------------------------------------- # Stage 2.3: NVT integration for 100 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 WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888) thermo ${Nthermo} thermo 0 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 10000 10000 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 2.3_averages.txt off 1 fix 3 movable ave/time 10 1 10 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 2.3_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 100000 2.3.restart dump sci all custom 10000 2.3.xyz id mol type q xs ys zs group rdfgroup_1 union subset_jiemian-k subset_jiemian-oh 103 atoms in group rdfgroup_1 compute rdf_1 rdfgroup_1 rdf 200 3 7 fix rdf_1 rdfgroup_1 ave/time 1 1000 1000 c_rdf_1[*] file 2.3_PairCorrelation_all_1.out mode vector group rdfgroup_3 union subset_jiemian-na subset_jiemian-oh 104 atoms in group rdfgroup_3 compute rdf_3 rdfgroup_3 rdf 200 6 7 fix rdf_3 rdfgroup_3 ave/time 1 1000 1000 c_rdf_3[*] file 2.3_PairCorrelation_all_3.out mode vector group rdfgroup_4 union subset_jiemian-Cl subset_jiemian-ho 221 atoms in group rdfgroup_4 compute rdf_4 rdfgroup_4 rdf 200 1 2 fix rdf_4 rdfgroup_4 ave/time 1 1000 1000 c_rdf_4[*] file 2.3_PairCorrelation_all_4.out mode vector group rdfgroup_6 union subset_jiemian7-na subset_jiemian7-oh 107 atoms in group rdfgroup_6 compute rdf_6 rdfgroup_6 rdf 200 6 7 fix rdf_6 rdfgroup_6 ave/time 1 1000 1000 c_rdf_6[*] file 2.3_PairCorrelation_all_6.out mode vector group rdfgroup_9 union subset_jiemian7-K subset_jiemian7-oh 106 atoms in group rdfgroup_9 compute rdf_9 rdfgroup_9 rdf 200 3 7 fix rdf_9 rdfgroup_9 ave/time 1 1000 1000 c_rdf_9[*] file 2.3_PairCorrelation_all_9.out mode vector group rdfgroup_10 union subset_jiemian7-cl subset_jiemian7-ho 236 atoms in group rdfgroup_10 compute rdf_10 rdfgroup_10 rdf 200 1 2 fix rdf_10 rdfgroup_10 ave/time 1 1000 1000 c_rdf_10[*] file 2.3_PairCorrelation_all_10.out mode vector compute group_29 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_29 all ave/time 1 100 100 c_group_29 file 2.3_GroupInteractions_Layer1_Layer2_29.out timestep 1 run 100000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0151 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 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 = 6 6 15 8 neighbor lists, perpetual/occasional/extra = 1 7 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 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 0.000197828 8436 2 103.7 0.0169358 2812 Per MPI rank memory allocation (min/avg/max) = 12.47 | 13.13 | 13.63 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 -451.85028 141184.09 1.4079299 407.8254 31.458002 74.509019 0 0 32041.753 -35694.065 -312.04795 -284080.19 -287626.53 9325.2516 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.27905e-06 8436 2 103.7 9.23988e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.17911e-06 8436 2 103.7 9.94563e-05 2812 100000 100000 -117.24537 141184.09 1.4079299 299.13918 51.296619 55.602175 0 0 31988.882 -35685.314 -312.04795 -284066.16 -287655.69 6840.0547 Loop time of 1371.6 on 32 procs for 100000 steps with 10808 atoms Performance: 6.299 ns/day, 3.810 hours/ns, 72.907 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 130.35 | 452.09 | 639.97 | 895.0 | 32.96 Bond | 0.11777 | 0.31809 | 0.7251 | 27.7 | 0.02 Kspace | 177.31 | 365.98 | 690.19 |1000.2 | 26.68 Neigh | 45.214 | 45.291 | 45.441 | 1.0 | 3.30 Comm | 39.85 | 53.252 | 58.399 | 80.8 | 3.88 Output | 0.012433 | 0.014918 | 0.017282 | 1.2 | 0.00 Modify | 447.89 | 451.89 | 462.22 | 22.4 | 32.95 Other | | 2.769 | | | 0.20 Nlocal: 337.75 ave 414 max 160 min Histogram: 4 4 0 0 0 0 0 4 5 15 Nghost: 6458.91 ave 7757 max 4762 min Histogram: 8 0 0 5 3 0 0 0 8 8 Neighs: 158248 ave 225339 max 44109 min Histogram: 8 0 0 0 0 3 1 4 5 11 Total # of neighbors = 5063937 Ave neighs/atom = 468.53599 Ave special neighs/atom = 1.6184308 Neighbor list builds = 4982 Dangerous builds = 0 undump sci restart 0 dump sci all custom 100000 2.3.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) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.17911e-06 8436 2 103.7 9.94563e-05 2812 Per MPI rank memory allocation (min/avg/max) = 15.14 | 19.36 | 21.65 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 100000 100000 -116.62074 141184.09 1.4079299 299.13918 51.296619 55.602175 0 0 31988.882 -35685.314 -312.04795 -284066.16 -287655.69 6840.0547 Loop time of 7.90656e-06 on 32 procs for 0 steps with 10808 atoms 116.2% 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 | | 7.907e-06 | | |100.00 Nlocal: 337.75 ave 414 max 160 min Histogram: 4 4 0 0 0 0 0 4 5 15 Nghost: 6458.91 ave 7757 max 4762 min Histogram: 8 0 0 5 3 0 0 0 8 8 Neighs: 158248 ave 225339 max 44109 min Histogram: 8 0 0 0 0 3 1 4 5 11 Total # of neighbors = 5063937 Ave neighs/atom = 468.53599 Ave special neighs/atom = 1.6184308 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute rdf_1 unfix rdf_1 group rdfgroup_1 delete uncompute rdf_3 unfix rdf_3 group rdfgroup_3 delete uncompute rdf_4 unfix rdf_4 group rdfgroup_4 delete uncompute rdf_6 unfix rdf_6 group rdfgroup_6 delete uncompute rdf_9 unfix rdf_9 group rdfgroup_9 delete uncompute rdf_10 unfix rdf_10 group rdfgroup_10 delete uncompute group_29 unfix group_29 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 0:22:51