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 = 3.1599882 3.1599882 3.1599882 Created orthogonal box = (0.0000000 -41.442857 0.0000000) to (29.304525 41.442857 4.4688982) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4520047 5.3008305 4.4688982 Created 343 atoms using lattice units in orthogonal box = (0.0000000 -41.442857 0.0000000) to (29.304525 41.442857 4.4688982) create_atoms CPU = 0.001 seconds 343 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4520047 5.3008305 4.4688982 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -41.442857 0.0000000) to (29.304525 41.442857 4.4688982) create_atoms CPU = 0.001 seconds 345 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 9 26 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 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 688 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_698578166685_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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15257.091 0 -15257.091 49452.647 57 0 -15387.574 0 -15387.574 19653.695 Loop time of 18.641 on 1 procs for 57 steps with 688 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 = -15257.0907863909 -15387.5584337189 -15387.5736062182 Force two-norm initial, final = 127.91415 0.49925203 Force max component initial, final = 26.757444 0.16723238 Final line search alpha, max atom move = 0.71188639 0.11905045 Iterations, force evaluations = 57 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.626 | 18.626 | 18.626 | 0.0 | 99.92 Neigh | 0.0077545 | 0.0077545 | 0.0077545 | 0.0 | 0.04 Comm | 0.0038802 | 0.0038802 | 0.0038802 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00384 | | | 0.02 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3952.00 ave 3952 max 3952 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: 44260.0 ave 44260 max 44260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44260 Ave neighs/atom = 64.331395 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -15387.574 0 -15387.574 19653.695 10854.625 64 0 -15388.281 0 -15388.281 -247.16799 10937.351 Loop time of 1.93423 on 1 procs for 7 steps with 688 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15387.5736062182 -15388.2762331193 -15388.2806970042 Force two-norm initial, final = 245.32361 3.0263866 Force max component initial, final = 199.35117 2.1445425 Final line search alpha, max atom move = 9.6930594e-05 0.00020787177 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9326 | 1.9326 | 1.9326 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027725 | 0.00027725 | 0.00027725 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00135 | | | 0.07 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3944.00 ave 3944 max 3944 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: 44276.0 ave 44276 max 44276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44276 Ave neighs/atom = 64.354651 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15388.281 0 -15388.281 -247.16799 Loop time of 1.683e-06 on 1 procs for 0 steps with 688 atoms 178.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.683e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3916.00 ave 3916 max 3916 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: 44210.0 ave 44210 max 44210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44210 Ave neighs/atom = 64.258721 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.646 | 4.646 | 4.646 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 -15388.281 -15388.281 29.342574 83.43715 4.4673961 -247.16799 -247.16799 -314.55486 -203.555 -223.39411 2.485849 480.66621 Loop time of 2.097e-06 on 1 procs for 0 steps with 688 atoms 238.4% 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 | | 2.097e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3916.00 ave 3916 max 3916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22105.0 ave 22105 max 22105 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44210.0 ave 44210 max 44210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44210 Ave neighs/atom = 64.258721 Neighbor list builds = 0 Dangerous builds = 0 688 -3502.533158809 eV 2.48584897210696 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21