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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -62.432665 0.0000000) to (25.486557 62.432665 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1167738 5.4105186 5.8858683 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -62.432665 0.0000000) to (25.486557 62.432665 8.8288024) create_atoms CPU = 0.002 seconds 1203 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1167738 5.4105186 5.8858683 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -62.432665 0.0000000) to (25.486557 62.432665 8.8288024) create_atoms CPU = 0.001 seconds 1203 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 41 3 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2384 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.176 | 5.176 | 5.176 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10048.481 0 -10048.481 1075.3423 702 0 -10133.813 0 -10133.813 -10434.572 Loop time of 104.227 on 1 procs for 702 steps with 2384 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 = -10048.4808252954 -10133.8052742187 -10133.8131584628 Force two-norm initial, final = 35.140036 0.24944186 Force max component initial, final = 5.7679116 0.035623428 Final line search alpha, max atom move = 0.81226071 0.028935511 Iterations, force evaluations = 702 1353 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 103.66 | 103.66 | 103.66 | 0.0 | 99.46 Neigh | 0.33042 | 0.33042 | 0.33042 | 0.0 | 0.32 Comm | 0.095624 | 0.095624 | 0.095624 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1365 | | | 0.13 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6883.00 ave 6883 max 6883 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: 173600.0 ave 173600 max 173600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173600 Ave neighs/atom = 72.818792 Neighbor list builds = 22 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 702 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.176 | 5.176 | 5.176 Mbytes Step Temp E_pair E_mol TotEng Press Volume 702 0 -10133.813 0 -10133.813 -10434.572 28096.67 727 0 -10145.458 0 -10145.458 8062.0949 27761.408 Loop time of 2.18786 on 1 procs for 25 steps with 2384 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 = -10133.8131584628 -10145.452851132 -10145.4578124502 Force two-norm initial, final = 909.25207 1.4180420 Force max component initial, final = 904.13923 0.17000515 Final line search alpha, max atom move = 8.0456237e-05 1.3677975e-05 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1754 | 2.1754 | 2.1754 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016972 | 0.0016972 | 0.0016972 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01079 | | | 0.49 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6875.00 ave 6875 max 6875 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: 173428.0 ave 173428 max 173428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173428 Ave neighs/atom = 72.746644 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.314 | 5.314 | 5.314 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10145.458 0 -10145.458 8062.0949 Loop time of 1.975e-06 on 1 procs for 0 steps with 2384 atoms 151.9% 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 | | 1.975e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6897.00 ave 6897 max 6897 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: 188262.0 ave 188262 max 188262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188262 Ave neighs/atom = 78.968960 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.314 | 5.314 | 5.314 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 -10145.458 -10145.458 24.872776 124.86533 8.9387206 8062.0949 8062.0949 0.70991116 24195.508 -9.9335507 2.3617381 13805.906 Loop time of 1.927e-06 on 1 procs for 0 steps with 2384 atoms 259.5% 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 | | 1.927e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6897.00 ave 6897 max 6897 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94131.0 ave 94131 max 94131 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188262.0 ave 188262 max 188262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188262 Ave neighs/atom = 78.968960 Neighbor list builds = 0 Dangerous builds = 0 2384 -10145.4578124502 eV 2.361738052293 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:47