LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.5898365 3.5898365 3.5898365 Created orthogonal box = (0.0000000 -62.177792 0.0000000) to (25.383977 62.177792 8.7932676) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0921545 5.3887419 5.8621784 Created 1199 atoms using lattice units in orthogonal box = (0.0000000 -62.177792 0.0000000) to (25.383977 62.177792 8.7932676) create_atoms CPU = 0.002 seconds 1199 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0921545 5.3887419 5.8621784 Created 1207 atoms using lattice units in orthogonal box = (0.0000000 -62.177792 0.0000000) to (25.383977 62.177792 8.7932676) create_atoms CPU = 0.002 seconds 1207 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 7 33 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2400 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_115316750986_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.473 | 6.473 | 6.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7132.93 0 -7132.93 80980.29 114 0 -8421.7288 0 -8421.7288 3759.7275 Loop time of 7.36913 on 1 procs for 114 steps with 2400 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7132.92996354149 -8421.7219443734 -8421.72877462494 Force two-norm initial, final = 1460.6189 0.26529406 Force max component initial, final = 220.84940 0.044933514 Final line search alpha, max atom move = 1.0000000 0.044933514 Iterations, force evaluations = 114 210 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2627 | 7.2627 | 7.2627 | 0.0 | 98.56 Neigh | 0.050833 | 0.050833 | 0.050833 | 0.0 | 0.69 Comm | 0.024096 | 0.024096 | 0.024096 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03145 | | | 0.43 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9430.00 ave 9430 max 9430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 392642.0 ave 392642 max 392642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 392642 Ave neighs/atom = 163.60083 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.470 | 6.470 | 6.470 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -8421.7288 0 -8421.7288 3759.7275 27757.174 120 0 -8422.1415 0 -8422.1415 -60.836384 27835.15 Loop time of 0.289091 on 1 procs for 6 steps with 2400 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8421.72877462494 -8422.14129155663 -8422.14153494134 Force two-norm initial, final = 170.36549 2.4515493 Force max component initial, final = 169.33122 2.2545945 Final line search alpha, max atom move = 0.00026117653 0.00058884717 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28465 | 0.28465 | 0.28465 | 0.0 | 98.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061508 | 0.00061508 | 0.00061508 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003823 | | | 1.32 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9082.00 ave 9082 max 9082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 405110.0 ave 405110 max 405110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 405110 Ave neighs/atom = 168.79583 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.608 | 6.608 | 6.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8422.1415 0 -8422.1415 -60.836384 Loop time of 2.228e-06 on 1 procs for 0 steps with 2400 atoms 179.5% CPU use with 1 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 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 | | 2.228e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9082.00 ave 9082 max 9082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 396962.0 ave 396962 max 396962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 396962 Ave neighs/atom = 165.40083 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.608 | 6.608 | 6.608 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -8422.1415 -8422.1415 25.359585 124.98825 8.7817735 -60.836384 -60.836384 -51.035213 -1.8703047 -129.60363 2.3993376 934.24834 Loop time of 1.0104e-05 on 1 procs for 0 steps with 2400 atoms 158.4% CPU use with 1 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 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 | | 1.01e-05 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9082.00 ave 9082 max 9082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 198481.0 ave 198481 max 198481 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 396962.0 ave 396962 max 396962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 396962 Ave neighs/atom = 165.40083 Neighbor list builds = 0 Dangerous builds = 0 2400 -8422.14153494134 eV 2.39933758078834 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08