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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -39.487209 0.0000000) to (8.0595571 39.487209 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8357343 5.2644806 5.8858683 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.487209 0.0000000) to (8.0595571 39.487209 8.8288024) create_atoms CPU = 0.001 seconds 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8357343 5.2644806 5.8858683 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.487209 0.0000000) to (8.0595571 39.487209 8.8288024) create_atoms CPU = 0.001 seconds 242 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 3 27 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 476 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_492310898779_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 3 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1999.0228 0 -1999.0228 3290.8984 40 0 -2013.1607 0 -2013.1607 -8213.5843 Loop time of 1.28663 on 1 procs for 40 steps with 476 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1999.02280270309 -2013.15917310289 -2013.16074374997 Force two-norm initial, final = 22.265373 0.11456692 Force max component initial, final = 6.5490319 0.015744312 Final line search alpha, max atom move = 1.0000000 0.015744312 Iterations, force evaluations = 40 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2821 | 1.2821 | 1.2821 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020178 | 0.0020178 | 0.0020178 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002527 | | | 0.20 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2840.00 ave 2840 max 2840 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: 36736.0 ave 36736 max 36736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36736 Ave neighs/atom = 77.176471 Neighbor list builds = 0 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 3 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.467 | 4.467 | 4.467 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -2013.1607 0 -2013.1607 -8213.5843 5619.5225 43 0 -2013.1943 0 -2013.1943 -3034.4192 5601.1803 Loop time of 0.110919 on 1 procs for 3 steps with 476 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2013.16074374997 -2013.19373552774 -2013.19433098066 Force two-norm initial, final = 28.052195 0.12358905 Force max component initial, final = 21.746053 0.016679568 Final line search alpha, max atom move = 0.00057561650 9.6010347e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11003 | 0.11003 | 0.11003 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014868 | 0.00014868 | 0.00014868 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007379 | | | 0.67 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2818.00 ave 2818 max 2818 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: 36844.0 ave 36844 max 36844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36844 Ave neighs/atom = 77.403361 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 3 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.605 | 4.605 | 4.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2013.1943 0 -2013.1943 -3034.4192 Loop time of 2.238e-06 on 1 procs for 0 steps with 476 atoms 178.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 2.238e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2820.00 ave 2820 max 2820 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: 36856.0 ave 36856 max 36856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36856 Ave neighs/atom = 77.428571 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 3 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.605 | 4.605 | 4.605 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 -2013.1943 -2013.1943 8.0412893 78.974418 8.8199766 -3034.4192 -3034.4192 1.7443428 -9103.7711 -1.2307313 2.2997134 264.26225 Loop time of 2.761e-06 on 1 procs for 0 steps with 476 atoms 181.1% 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 | | 2.761e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2820.00 ave 2820 max 2820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18428.0 ave 18428 max 18428 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36856.0 ave 36856 max 36856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36856 Ave neighs/atom = 77.428571 Neighbor list builds = 0 Dangerous builds = 0 476 -2013.19433098066 eV 2.29971336768978 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01