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 = 3.6084290 3.6084290 3.6084290 Created orthogonal box = (0.0000000 -44.194050 0.0000000) to (6.2499824 44.194050 5.1030893) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2499824 5.8925399 5.1030893 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -44.194050 0.0000000) to (6.2499824 44.194050 5.1030893) create_atoms CPU = 0.001 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2499824 5.8925399 5.1030893 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -44.194050 0.0000000) to (6.2499824 44.194050 5.1030893) create_atoms CPU = 0.001 seconds 122 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 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_549900287421_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 30 2 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) = 4.442 | 4.442 | 4.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1007.02 0 -1007.02 16898.809 325 0 -1023.8586 0 -1023.8586 1872.784 Loop time of 6.80038 on 1 procs for 325 steps with 240 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1007.02004075029 -1023.85768125062 -1023.85864679522 Force two-norm initial, final = 30.115043 0.062009377 Force max component initial, final = 9.2953376 0.0078053171 Final line search alpha, max atom move = 1.0000000 0.0078053171 Iterations, force evaluations = 325 641 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.7609 | 6.7609 | 6.7609 | 0.0 | 99.42 Neigh | 0.009036 | 0.009036 | 0.009036 | 0.0 | 0.13 Comm | 0.018382 | 0.018382 | 0.018382 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01203 | | | 0.18 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2574.00 ave 2574 max 2574 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: 17754.0 ave 17754 max 17754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17754 Ave neighs/atom = 73.975000 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 3 30 2 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 : 325 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 325 0 -1023.8586 0 -1023.8586 1872.784 2819.0693 347 0 -1024.7123 0 -1024.7123 6.0561091 2819.9051 Loop time of 0.217635 on 1 procs for 22 steps with 240 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 = -1023.85864679522 -1024.71163656782 -1024.71234640505 Force two-norm initial, final = 62.137829 1.7518997 Force max component initial, final = 45.929722 1.2316728 Final line search alpha, max atom move = 0.0060789999 0.0074873391 Iterations, force evaluations = 22 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21362 | 0.21362 | 0.21362 | 0.0 | 98.16 Neigh | 0.0013224 | 0.0013224 | 0.0013224 | 0.0 | 0.61 Comm | 0.00057619 | 0.00057619 | 0.00057619 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002113 | | | 0.97 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2539.00 ave 2539 max 2539 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: 17224.0 ave 17224 max 17224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17224 Ave neighs/atom = 71.766667 Neighbor list builds = 1 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 29 2 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) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1024.7123 0 -1024.7123 6.0561091 Loop time of 1.578e-06 on 1 procs for 0 steps with 240 atoms 190.1% 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 | | 1.578e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2539.00 ave 2539 max 2539 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: 17192.0 ave 17192 max 17192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17192 Ave neighs/atom = 71.633333 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 29 2 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) = 4.579 | 4.579 | 4.579 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 -1024.7123 -1024.7123 6.3587527 86.536174 5.1246577 6.0561091 6.0561091 628.42654 92.495147 -702.75336 2.4167467 1056.0957 Loop time of 1.463e-06 on 1 procs for 0 steps with 240 atoms 205.1% 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 | | 1.463e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2539.00 ave 2539 max 2539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8596.00 ave 8596 max 8596 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17192.0 ave 17192 max 17192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17192 Ave neighs/atom = 71.633333 Neighbor list builds = 0 Dangerous builds = 0 240 -1024.71234640505 eV 2.41674668867938 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07