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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -33.001389 0.0000000) to (40.418282 33.001389 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1441450 4.8002020 5.1383093 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -33.001389 0.0000000) to (40.418282 33.001389 7.7074639) create_atoms CPU = 0.001 seconds 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1441450 4.8002020 5.1383093 Created 664 atoms using lattice units in orthogonal box = (0.0000000 -33.001389 0.0000000) to (40.418282 33.001389 7.7074639) create_atoms CPU = 0.001 seconds 664 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 21 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1320 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_356501945107_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.596 | 4.596 | 4.596 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5793.4654 0 -5793.4654 370926.21 99 0 -8916.6559 0 -8916.6559 14880.655 Loop time of 6.66935 on 1 procs for 99 steps with 1320 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5793.46544279802 -8916.64740513355 -8916.65591231997 Force two-norm initial, final = 2428.9396 0.52632150 Force max component initial, final = 335.76253 0.075250068 Final line search alpha, max atom move = 0.93594211 0.070429707 Iterations, force evaluations = 99 172 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6245 | 6.6245 | 6.6245 | 0.0 | 99.33 Neigh | 0.024536 | 0.024536 | 0.024536 | 0.0 | 0.37 Comm | 0.0079498 | 0.0079498 | 0.0079498 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01238 | | | 0.19 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4244.00 ave 4244 max 4244 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: 84784.0 ave 84784 max 84784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84784 Ave neighs/atom = 64.230303 Neighbor list builds = 3 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.596 | 4.596 | 4.596 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -8916.6559 0 -8916.6559 14880.655 20561.347 106 0 -8917.7877 0 -8917.7877 -294.8222 20679.214 Loop time of 0.306631 on 1 procs for 7 steps with 1320 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 = -8916.65591231996 -8917.78622681027 -8917.78770981874 Force two-norm initial, final = 382.63855 7.7138930 Force max component initial, final = 319.70794 6.8507550 Final line search alpha, max atom move = 0.00010165472 0.00069641160 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30459 | 0.30459 | 0.30459 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029275 | 0.00029275 | 0.00029275 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001751 | | | 0.57 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4247.00 ave 4247 max 4247 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: 84776.0 ave 84776 max 84776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84776 Ave neighs/atom = 64.224242 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.734 | 4.734 | 4.734 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8917.7877 0 -8917.7877 -294.8222 Loop time of 2.105e-06 on 1 procs for 0 steps with 1320 atoms 142.5% 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 | | 2.105e-06 | | |100.00 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4244.00 ave 4244 max 4244 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: 84688.0 ave 84688 max 84688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84688 Ave neighs/atom = 64.157576 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.734 | 4.734 | 4.734 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 -8917.7877 -8917.7877 40.517256 66.395955 7.6869201 -294.8222 -294.8222 -238.37837 -116.72271 -529.36551 2.5033564 1794.9708 Loop time of 1.851e-06 on 1 procs for 0 steps with 1320 atoms 162.1% 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 | | 1.851e-06 | | |100.00 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4244.00 ave 4244 max 4244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42344.0 ave 42344 max 42344 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84688.0 ave 84688 max 84688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84688 Ave neighs/atom = 64.157576 Neighbor list builds = 0 Dangerous builds = 0 1320 -8917.78770981874 eV 2.50335639572561 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07