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 = 3.1409628 3.1409628 3.1409628 Created orthogonal box = (0.0000000 -38.851564 0.0000000) to (12.950521 38.851564 3.1409628) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8089769 3.8089769 3.1409628 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -38.851564 0.0000000) to (12.950521 38.851564 3.1409628) create_atoms CPU = 0.001 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8089769 3.8089769 3.1409628 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -38.851564 0.0000000) to (12.950521 38.851564 3.1409628) create_atoms CPU = 0.000 seconds 103 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 3 14 1 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 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 204 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_666830945336_004#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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 3 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -902.39533 0 -902.39533 295625.73 98 0 -1366.7554 0 -1366.7554 18341.996 Loop time of 0.857577 on 1 procs for 98 steps with 204 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -902.39532752335 -1366.75412766382 -1366.75536673929 Force two-norm initial, final = 1330.1641 0.20134288 Force max component initial, final = 470.77102 0.032838733 Final line search alpha, max atom move = 0.98679877 0.032405221 Iterations, force evaluations = 98 183 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83565 | 0.83565 | 0.83565 | 0.0 | 97.44 Neigh | 0.0091831 | 0.0091831 | 0.0091831 | 0.0 | 1.07 Comm | 0.0089637 | 0.0089637 | 0.0089637 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003783 | | | 0.44 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5668.00 ave 5668 max 5668 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: 83400.0 ave 83400 max 83400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83400 Ave neighs/atom = 408.82353 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 3 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.470 | 4.470 | 4.470 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -1366.7554 0 -1366.7554 18341.996 3160.7384 956 0 -1388.0098 0 -1388.0098 539.12149 3158.4237 Loop time of 5.08995 on 1 procs for 858 steps with 204 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1366.75536673929 -1388.00848103725 -1388.0098105674 Force two-norm initial, final = 110.59093 3.4056173 Force max component initial, final = 85.822447 1.1603333 Final line search alpha, max atom move = 0.00022163231 0.00025716736 Iterations, force evaluations = 858 1082 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7869 | 4.7869 | 4.7869 | 0.0 | 94.05 Neigh | 0.033431 | 0.033431 | 0.033431 | 0.0 | 0.66 Comm | 0.051921 | 0.051921 | 0.051921 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2177 | | | 4.28 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6267.00 ave 6267 max 6267 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: 84180.0 ave 84180 max 84180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84180 Ave neighs/atom = 412.64706 Neighbor list builds = 7 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 4.622 | 4.622 | 4.622 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1388.0098 0 -1388.0098 539.12149 Loop time of 8.997e-06 on 1 procs for 0 steps with 204 atoms 133.4% 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 | | 8.997e-06 | | |100.00 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6267.00 ave 6267 max 6267 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: 84268.0 ave 84268 max 84268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84268 Ave neighs/atom = 413.07843 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 4.622 | 4.622 | 4.622 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 -1388.0098 -1388.0098 13.120378 85.351447 2.820416 539.12149 539.12149 596.32335 618.89161 402.1495 2.628177 911.77948 Loop time of 2.147e-06 on 1 procs for 0 steps with 204 atoms 186.3% 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 | | 2.147e-06 | | |100.00 Nlocal: 204.000 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6267.00 ave 6267 max 6267 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42134.0 ave 42134 max 42134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84268.0 ave 84268 max 84268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84268 Ave neighs/atom = 413.07843 Neighbor list builds = 0 Dangerous builds = 0 204 -1388.0098105674 eV 2.62817697828755 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06