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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -77.390376 0.0000000) to (44.681355 77.390376 7.0065955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5923310 5.9205752 7.0065955 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -77.390376 0.0000000) to (44.681355 77.390376 7.0065955) create_atoms CPU = 0.009 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5923310 5.9205752 7.0065955 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.390376 0.0000000) to (44.681355 77.390376 7.0065955) create_atoms CPU = 0.009 seconds 1465 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 37 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2924 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_106969701023_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.606 | 6.606 | 6.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9807.1159 0 -9807.1159 10088.257 70 0 -9949.0069 0 -9949.0069 2996.5806 Loop time of 6.8737 on 1 procs for 70 steps with 2924 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 = -9807.11592379113 -9948.99895291014 -9949.00694128787 Force two-norm initial, final = 176.63158 0.18068307 Force max component initial, final = 65.037581 0.032263832 Final line search alpha, max atom move = 1.0000000 0.032263832 Iterations, force evaluations = 70 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6082 | 6.6082 | 6.6082 | 0.0 | 96.14 Neigh | 0.18676 | 0.18676 | 0.18676 | 0.0 | 2.72 Comm | 0.040354 | 0.040354 | 0.040354 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03838 | | | 0.56 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11952.0 ave 11952 max 11952 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: 412600.0 ave 412600 max 412600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412600 Ave neighs/atom = 141.10807 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.606 | 6.606 | 6.606 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -9949.0069 0 -9949.0069 2996.5806 48456.309 75 0 -9949.3029 0 -9949.3029 -4.1005201 48637.732 Loop time of 0.427245 on 1 procs for 5 steps with 2924 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 = -9949.0069412879 -9949.29974998104 -9949.30294225803 Force two-norm initial, final = 172.20290 0.83779474 Force max component initial, final = 148.38215 0.66950192 Final line search alpha, max atom move = 4.4715946e-05 2.9937412e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41703 | 0.41703 | 0.41703 | 0.0 | 97.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002148 | 0.002148 | 0.002148 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008064 | | | 1.89 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11952.0 ave 11952 max 11952 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: 412420.0 ave 412420 max 412420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412420 Ave neighs/atom = 141.04651 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.744 | 6.744 | 6.744 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9949.3029 0 -9949.3029 -4.1005201 Loop time of 6.616e-06 on 1 procs for 0 steps with 2924 atoms 181.4% 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 | | 6.616e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11952.0 ave 11952 max 11952 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: 411812.0 ave 411812 max 411812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411812 Ave neighs/atom = 140.83858 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.744 | 6.744 | 6.744 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 -9949.3029 -9949.3029 44.662133 155.43735 7.0061344 -4.1005201 -4.1005201 -22.044589 -4.330438 14.073466 2.4291374 1229.8928 Loop time of 6.936e-06 on 1 procs for 0 steps with 2924 atoms 245.1% 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 | | 6.936e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11952.0 ave 11952 max 11952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 205906.0 ave 205906 max 205906 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 411812.0 ave 411812 max 411812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411812 Ave neighs/atom = 140.83858 Neighbor list builds = 0 Dangerous builds = 0 2924 -9949.30294225803 eV 2.42913739293521 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08