LAMMPS (2 Aug 2023 - Update 1) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 2 Aug 2023 # Lattice spacing in x,y,z = 5.1529356 5.1529356 5.1529356 Created orthogonal box = (0 0 0) to (51.529356 51.529356 51.529356) 1 by 1 by 1 MPI processor grid Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (51.529356 51.529356 51.529356) create_atoms CPU = 0.001 seconds WARNING: Van der Waals parameters for element SI indicate inner wall+shielding, but earlier atoms indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (src/REAXFF/reaxff_ffield.cpp:251) WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:296) Initial system volume: 136824.58903756 Angstroms^3 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM Project: doi:10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/SM_282799919035_000#item-citation - pair reaxff command: doi:10.1016/j.parco.2011.08.005 - fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005 The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 9 9 9 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reaxff, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reaxff, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 302 | 302 | 302 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -365743.67 -15860.146 -369238.09 -16011.679 293.15 293.15 136824.59 136824.59 1167.4846 1182.9538 1000 -362482.08 -15718.711 -365912.6 -15867.472 287.78827 287.78827 160391.67 160391.67 132.29948 134.05245 Loop time of 171.991 on 1 procs for 1000 steps with 4000 atoms Performance: 0.502 ns/day, 47.775 hours/ns, 5.814 timesteps/s, 23.257 katom-step/s 88.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 155.42 | 155.42 | 155.42 | 0.0 | 90.37 Neigh | 0.36711 | 0.36711 | 0.36711 | 0.0 | 0.21 Comm | 0.036638 | 0.036638 | 0.036638 | 0.0 | 0.02 Output | 0.00010793 | 0.00010793 | 0.00010793 | 0.0 | 0.00 Modify | 16.122 | 16.122 | 16.122 | 0.0 | 9.37 Other | | 0.04196 | | | 0.02 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 447327 ave 447327 max 447327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 447327 Ave neighs/atom = 111.83175 Neighbor list builds = 9 Dangerous builds = 0 flag: Temp = 292.666646859522, Press = 5.98926572843805 Setting up Verlet run ... Unit style : real Current step : 1000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -362482.08 -15718.711 -365912.6 -15867.472 287.78827 287.78827 160391.67 160391.67 132.29948 134.05245 2000 -362301.97 -15710.9 -365791.12 -15862.204 292.70762 292.70762 160765.19 160765.19 -1581.6082 -1602.5645 Loop time of 140.814 on 1 procs for 1000 steps with 4000 atoms Performance: 0.614 ns/day, 39.115 hours/ns, 7.102 timesteps/s, 28.406 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 126.77 | 126.77 | 126.77 | 0.0 | 90.03 Neigh | 0.13801 | 0.13801 | 0.13801 | 0.0 | 0.10 Comm | 0.033369 | 0.033369 | 0.033369 | 0.0 | 0.02 Output | 6.2026e-05 | 6.2026e-05 | 6.2026e-05 | 0.0 | 0.00 Modify | 13.852 | 13.852 | 13.852 | 0.0 | 9.84 Other | | 0.01897 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 446625 ave 446625 max 446625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 446625 Ave neighs/atom = 111.65625 Neighbor list builds = 5 Dangerous builds = 0 flag: Temp = 293.301561621513, Press = -14.0958995817587 Setting up Verlet run ... Unit style : real Current step : 2000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -362301.97 -15710.9 -365791.12 -15862.204 292.70762 292.70762 160765.19 160765.19 -1581.6082 -1602.5645 3000 -362191.51 -15706.11 -365597.6 -15853.812 285.73919 285.73919 160593.1 160593.1 -267.79341 -271.34167 Loop time of 147.558 on 1 procs for 1000 steps with 4000 atoms Performance: 0.586 ns/day, 40.988 hours/ns, 6.777 timesteps/s, 27.108 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 133.53 | 133.53 | 133.53 | 0.0 | 90.49 Neigh | 0.11138 | 0.11138 | 0.11138 | 0.0 | 0.08 Comm | 0.03477 | 0.03477 | 0.03477 | 0.0 | 0.02 Output | 5.849e-05 | 5.849e-05 | 5.849e-05 | 0.0 | 0.00 Modify | 13.865 | 13.865 | 13.865 | 0.0 | 9.40 Other | | 0.02065 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 446598 ave 446598 max 446598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 446598 Ave neighs/atom = 111.6495 Neighbor list builds = 4 Dangerous builds = 0 flag: Temp = 293.255787844148, Press = -9.91669741643013 Setting up Verlet run ... Unit style : real Current step : 3000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -362191.51 -15706.11 -365597.6 -15853.812 285.73919 285.73919 160593.1 160593.1 -267.79341 -271.34167 4000 -362173.42 -15705.326 -365688.03 -15857.734 294.84272 294.84272 160808.77 160808.77 -910.01843 -922.07618 Loop time of 144.911 on 1 procs for 1000 steps with 4000 atoms Performance: 0.596 ns/day, 40.253 hours/ns, 6.901 timesteps/s, 27.603 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 130.98 | 130.98 | 130.98 | 0.0 | 90.38 Neigh | 0.13908 | 0.13908 | 0.13908 | 0.0 | 0.10 Comm | 0.034599 | 0.034599 | 0.034599 | 0.0 | 0.02 Output | 5.3921e-05 | 5.3921e-05 | 5.3921e-05 | 0.0 | 0.00 Modify | 13.74 | 13.74 | 13.74 | 0.0 | 9.48 Other | | 0.02017 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 446581 ave 446581 max 446581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 446581 Ave neighs/atom = 111.64525 Neighbor list builds = 5 Dangerous builds = 0 flag: Temp = 293.066158942026, Press = -9.65459789880963 Setting up Verlet run ... Unit style : real Current step : 4000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -362173.42 -15705.326 -365688.03 -15857.734 294.84272 294.84272 160808.77 160808.77 -910.01843 -922.07618 5000 -362523.28 -15720.497 -365971.48 -15870.025 289.2717 289.2717 160778.73 160778.73 429.40803 435.09769 Loop time of 148.588 on 1 procs for 1000 steps with 4000 atoms Performance: 0.581 ns/day, 41.274 hours/ns, 6.730 timesteps/s, 26.920 katom-step/s 97.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 134.24 | 134.24 | 134.24 | 0.0 | 90.34 Neigh | 0.10992 | 0.10992 | 0.10992 | 0.0 | 0.07 Comm | 0.03421 | 0.03421 | 0.03421 | 0.0 | 0.02 Output | 6.4541e-05 | 6.4541e-05 | 6.4541e-05 | 0.0 | 0.00 Modify | 14.189 | 14.189 | 14.189 | 0.0 | 9.55 Other | | 0.01957 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 446798 ave 446798 max 446798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 446798 Ave neighs/atom = 111.6995 Neighbor list builds = 4 Dangerous builds = 0 flag: Temp = 293.136864510705, Press = -6.63090378071233 Setting up Verlet run ... Unit style : real Current step : 5000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -362523.28 -15720.497 -365971.48 -15870.025 289.2717 289.2717 160778.73 160778.73 429.40803 435.09769 6000 -362392.46 -15714.824 -365842.89 -15864.449 289.4594 289.4594 160460.14 160460.14 1400.8477 1419.409 Loop time of 148.118 on 1 procs for 1000 steps with 4000 atoms Performance: 0.583 ns/day, 41.144 hours/ns, 6.751 timesteps/s, 27.006 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 134.15 | 134.15 | 134.15 | 0.0 | 90.57 Neigh | 0.1385 | 0.1385 | 0.1385 | 0.0 | 0.09 Comm | 0.034979 | 0.034979 | 0.034979 | 0.0 | 0.02 Output | 5.9151e-05 | 5.9151e-05 | 5.9151e-05 | 0.0 | 0.00 Modify | 13.773 | 13.773 | 13.773 | 0.0 | 9.30 Other | | 0.02062 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 446674 ave 446674 max 446674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 446674 Ave neighs/atom = 111.6685 Neighbor list builds = 5 Dangerous builds = 0 flag: Temp = 293.097061707177, Press = -6.56495067269021 Setting up Verlet run ... Unit style : real Current step : 6000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -362392.46 -15714.824 -365842.89 -15864.449 289.4594 289.4594 160460.14 160460.14 1400.8477 1419.409 7000 -362223.61 -15707.502 -365763.85 -15861.022 296.99318 296.99318 160646.22 160646.22 382.21941 387.28382 Loop time of 146.763 on 1 procs for 1000 steps with 4000 atoms Performance: 0.589 ns/day, 40.767 hours/ns, 6.814 timesteps/s, 27.255 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 132.84 | 132.84 | 132.84 | 0.0 | 90.51 Neigh | 0.13849 | 0.13849 | 0.13849 | 0.0 | 0.09 Comm | 0.035175 | 0.035175 | 0.035175 | 0.0 | 0.02 Output | 5.7528e-05 | 5.7528e-05 | 5.7528e-05 | 0.0 | 0.00 Modify | 13.728 | 13.728 | 13.728 | 0.0 | 9.35 Other | | 0.0205 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 447208 ave 447208 max 447208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 447208 Ave neighs/atom = 111.802 Neighbor list builds = 5 Dangerous builds = 0 flag: Temp = 293.124937098236, Press = -7.41616484114544 Setting up Verlet run ... Unit style : real Current step : 7000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 7000 -362223.61 -15707.502 -365763.85 -15861.022 296.99318 296.99318 160646.22 160646.22 382.21941 387.28382 8000 -362183.89 -15705.78 -365724.49 -15859.315 297.02423 297.02423 160435.21 160435.21 1287.8473 1304.9113 Loop time of 146.493 on 1 procs for 1000 steps with 4000 atoms Performance: 0.590 ns/day, 40.692 hours/ns, 6.826 timesteps/s, 27.305 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 132.55 | 132.55 | 132.55 | 0.0 | 90.48 Neigh | 0.11128 | 0.11128 | 0.11128 | 0.0 | 0.08 Comm | 0.034613 | 0.034613 | 0.034613 | 0.0 | 0.02 Output | 7.3197e-05 | 7.3197e-05 | 7.3197e-05 | 0.0 | 0.00 Modify | 13.776 | 13.776 | 13.776 | 0.0 | 9.40 Other | | 0.02021 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 446419 ave 446419 max 446419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 446419 Ave neighs/atom = 111.60475 Neighbor list builds = 4 Dangerous builds = 0 flag: Temp = 293.12998389071, Press = -6.45095876278958 Setting up Verlet run ... Unit style : real Current step : 8000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 8000 -362183.89 -15705.78 -365724.49 -15859.315 297.02423 297.02423 160435.21 160435.21 1287.8473 1304.9113 9000 -362323.71 -15711.843 -365850.7 -15864.788 295.88204 295.88204 160647.09 160647.09 152.95841 154.98511 Loop time of 147.604 on 1 procs for 1000 steps with 4000 atoms Performance: 0.585 ns/day, 41.001 hours/ns, 6.775 timesteps/s, 27.099 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 133.61 | 133.61 | 133.61 | 0.0 | 90.52 Neigh | 0.14554 | 0.14554 | 0.14554 | 0.0 | 0.10 Comm | 0.035617 | 0.035617 | 0.035617 | 0.0 | 0.02 Output | 6.927e-05 | 6.927e-05 | 6.927e-05 | 0.0 | 0.00 Modify | 13.794 | 13.794 | 13.794 | 0.0 | 9.35 Other | | 0.02045 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 447088 ave 447088 max 447088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 447088 Ave neighs/atom = 111.772 Neighbor list builds = 5 Dangerous builds = 0 flag: Temp = 293.102880008371, Press = -5.23333947104644 Setting up Verlet run ... Unit style : real Current step : 9000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301 | 301 | 301 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 9000 -362323.71 -15711.843 -365850.7 -15864.788 295.88204 295.88204 160647.09 160647.09 152.95841 154.98511 10000 -362231.63 -15707.85 -365728.16 -15859.474 293.32683 293.32683 160680.88 160680.88 -370.13647 -375.04078 Loop time of 147.938 on 1 procs for 1000 steps with 4000 atoms Performance: 0.584 ns/day, 41.094 hours/ns, 6.760 timesteps/s, 27.038 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 133.81 | 133.81 | 133.81 | 0.0 | 90.45 Neigh | 0.11014 | 0.11014 | 0.11014 | 0.0 | 0.07 Comm | 0.03664 | 0.03664 | 0.03664 | 0.0 | 0.02 Output | 7.8217e-05 | 7.8217e-05 | 7.8217e-05 | 0.0 | 0.00 Modify | 13.955 | 13.955 | 13.955 | 0.0 | 9.43 Other | | 0.02092 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 446929 ave 446929 max 446929 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 446929 Ave neighs/atom = 111.73225 Neighbor list builds = 4 Dangerous builds = 0 160666.062429485 LAMMPS calculation completed