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 = 2.8669658 2.8669658 2.8669658 Created orthogonal box = (0.0000000 -56.765894 0.0000000) to (34.760113 56.765894 7.0226033) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0198770 4.0545019 4.6817355 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.765894 0.0000000) to (34.760113 56.765894 7.0226033) create_atoms CPU = 0.002 seconds 1182 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0198770 4.0545019 4.6817355 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.765894 0.0000000) to (34.760113 56.765894 7.0226033) create_atoms CPU = 0.001 seconds 1182 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 2363 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_677715648236_000#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.488 | 6.488 | 6.488 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8306.8707 0 -8306.8707 240096.95 347 0 -9528.8911 0 -9528.8911 -61379.386 Loop time of 11.4582 on 1 procs for 347 steps with 2363 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8306.87071203685 -9528.88243319002 -9528.89105168384 Force two-norm initial, final = 1059.7469 0.35945590 Force max component initial, final = 146.16673 0.10673940 Final line search alpha, max atom move = 1.0000000 0.10673940 Iterations, force evaluations = 347 686 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.274 | 11.274 | 11.274 | 0.0 | 98.39 Neigh | 0.064787 | 0.064787 | 0.064787 | 0.0 | 0.57 Comm | 0.05875 | 0.05875 | 0.05875 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06053 | | | 0.53 Nlocal: 2363.00 ave 2363 max 2363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9852.00 ave 9852 max 9852 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: 374732.0 ave 374732 max 374732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374732 Ave neighs/atom = 158.58316 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 347 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.111 | 6.111 | 6.111 Mbytes Step Temp E_pair E_mol TotEng Press Volume 347 0 -9528.8911 0 -9528.8911 -61379.386 27713.845 373 0 -9547.043 0 -9547.043 -19862.072 26727.635 Loop time of 0.492125 on 1 procs for 26 steps with 2363 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 = -9528.8910516838 -9547.0410059691 -9547.04300499884 Force two-norm initial, final = 1301.5112 7.3972071 Force max component initial, final = 1117.1965 4.2373135 Final line search alpha, max atom move = 0.00010119504 0.00042879512 Iterations, force evaluations = 26 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47833 | 0.47833 | 0.47833 | 0.0 | 97.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020346 | 0.0020346 | 0.0020346 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01176 | | | 2.39 Nlocal: 2363.00 ave 2363 max 2363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9857.00 ave 9857 max 9857 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: 372938.0 ave 372938 max 372938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372938 Ave neighs/atom = 157.82395 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.251 | 6.251 | 6.251 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9547.043 0 -9547.043 -19862.072 Loop time of 1.527e-06 on 1 procs for 0 steps with 2363 atoms 131.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.527e-06 | | |100.00 Nlocal: 2363.00 ave 2363 max 2363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10069.0 ave 10069 max 10069 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: 381642.0 ave 381642 max 381642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 381642 Ave neighs/atom = 161.50741 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.251 | 6.251 | 6.251 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 -9547.043 -9547.043 34.376649 113.53179 6.8482486 -19862.072 -19862.072 -251.20182 -59320.411 -14.601668 2.2682351 7368.4476 Loop time of 2.077e-06 on 1 procs for 0 steps with 2363 atoms 192.6% 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 | | 2.077e-06 | | |100.00 Nlocal: 2363.00 ave 2363 max 2363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10069.0 ave 10069 max 10069 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 190821.0 ave 190821 max 190821 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 381642.0 ave 381642 max 381642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 381642 Ave neighs/atom = 161.50741 Neighbor list builds = 0 Dangerous builds = 0 2363 -9547.04300499884 eV 2.26823509211003 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12