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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -45.251474 0.0000000) to (21.331749 45.251474 5.1737092) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2740440 6.2109866 5.1737092 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -45.251474 0.0000000) to (21.331749 45.251474 5.1737092) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2740440 6.2109866 5.1737092 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -45.251474 0.0000000) to (21.331749 45.251474 5.1737092) create_atoms CPU = 0.001 seconds 412 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 = 6 24 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 0 atoms, new total = 820 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_267721408934_005#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 = 6 24 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) = 4.970 | 4.970 | 4.970 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3074.1299 0 -3074.1299 81632.47 271 0 -3304.4027 0 -3304.4027 -36462.026 Loop time of 3.29703 on 1 procs for 271 steps with 820 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3074.1298568517 -3304.39962800251 -3304.40265253051 Force two-norm initial, final = 388.85272 0.17761466 Force max component initial, final = 73.826006 0.015882771 Final line search alpha, max atom move = 1.0000000 0.015882771 Iterations, force evaluations = 271 527 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2031 | 3.2031 | 3.2031 | 0.0 | 97.15 Neigh | 0.044746 | 0.044746 | 0.044746 | 0.0 | 1.36 Comm | 0.027697 | 0.027697 | 0.027697 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02147 | | | 0.65 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5365.00 ave 5365 max 5365 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: 121416.0 ave 121416 max 121416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121416 Ave neighs/atom = 148.06829 Neighbor list builds = 6 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 = 6 24 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 : 271 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.970 | 4.970 | 4.970 Mbytes Step Temp E_pair E_mol TotEng Press Volume 271 0 -3304.4027 0 -3304.4027 -36462.026 9988.2916 365 0 -3327.0548 0 -3327.0548 -476.62858 9839.928 Loop time of 0.664447 on 1 procs for 94 steps with 820 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 = -3304.40265253051 -3327.05333847852 -3327.05476633056 Force two-norm initial, final = 577.53768 6.5872254 Force max component initial, final = 524.86477 3.3967668 Final line search alpha, max atom move = 0.00038230005 0.0012985841 Iterations, force evaluations = 94 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60404 | 0.60404 | 0.60404 | 0.0 | 90.91 Neigh | 0.033043 | 0.033043 | 0.033043 | 0.0 | 4.97 Comm | 0.0051317 | 0.0051317 | 0.0051317 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02223 | | | 3.35 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5427.00 ave 5427 max 5427 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: 128088.0 ave 128088 max 128088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128088 Ave neighs/atom = 156.20488 Neighbor list builds = 4 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 = 6 23 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) = 5.109 | 5.109 | 5.109 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3327.0548 0 -3327.0548 -476.62858 Loop time of 1.816e-06 on 1 procs for 0 steps with 820 atoms 165.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.816e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5493.00 ave 5493 max 5493 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: 128576.0 ave 128576 max 128576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128576 Ave neighs/atom = 156.80000 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 = 6 23 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) = 5.109 | 5.109 | 5.109 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 -3327.0548 -3327.0548 20.672324 85.546756 5.5641532 -476.62858 -476.62858 -522.3866 -522.78724 -384.7119 2.3157653 1986.2182 Loop time of 2.064e-06 on 1 procs for 0 steps with 820 atoms 193.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 2.064e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5493.00 ave 5493 max 5493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64288.0 ave 64288 max 64288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128576.0 ave 128576 max 128576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128576 Ave neighs/atom = 156.80000 Neighbor list builds = 0 Dangerous builds = 0 820 -3327.05476633056 eV 2.31576533650521 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04