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 = 4.0499994 4.0499994 4.0499994 Created orthogonal box = (0.0000000 -41.302052 0.0000000) to (35.768627 41.302052 7.0148048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4200099 6.3541619 7.0148048 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -41.302052 0.0000000) to (35.768627 41.302052 7.0148048) create_atoms CPU = 0.002 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4200099 6.3541619 7.0148048 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -41.302052 0.0000000) to (35.768627 41.302052 7.0148048) create_atoms CPU = 0.001 seconds 630 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 19 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1247 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_117656786760_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.445 | 5.445 | 5.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4119.7681 0 -4119.7681 6561.3858 51 0 -4173.0463 0 -4173.0463 5543.2593 Loop time of 1.07329 on 1 procs for 51 steps with 1247 atoms 94.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4119.76806047626 -4173.0429307861 -4173.04629262221 Force two-norm initial, final = 37.128801 0.13477899 Force max component initial, final = 10.031968 0.018462672 Final line search alpha, max atom move = 1.0000000 0.018462672 Iterations, force evaluations = 51 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0205 | 1.0205 | 1.0205 | 0.0 | 95.09 Neigh | 0.040233 | 0.040233 | 0.040233 | 0.0 | 3.75 Comm | 0.0063923 | 0.0063923 | 0.0063923 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006125 | | | 0.57 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6204.00 ave 6204 max 6204 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: 216086.0 ave 216086 max 216086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216086 Ave neighs/atom = 173.28468 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.445 | 5.445 | 5.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -4173.0463 0 -4173.0463 5543.2593 20726.19 62 0 -4173.6509 0 -4173.6509 29.350298 20869.457 Loop time of 0.170133 on 1 procs for 11 steps with 1247 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4173.04629262219 -4173.65084989286 -4173.65086605114 Force two-norm initial, final = 145.96785 0.74917242 Force max component initial, final = 132.45745 0.44743889 Final line search alpha, max atom move = 0.0039604975 0.0017720806 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16513 | 0.16513 | 0.16513 | 0.0 | 97.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073002 | 0.00073002 | 0.00073002 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004268 | | | 2.51 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6204.00 ave 6204 max 6204 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: 216092.0 ave 216092 max 216092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216092 Ave neighs/atom = 173.28949 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.584 | 5.584 | 5.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4173.6509 0 -4173.6509 29.350298 Loop time of 1.731e-06 on 1 procs for 0 steps with 1247 atoms 173.3% 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 | | 1.731e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6204.00 ave 6204 max 6204 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: 215586.0 ave 215586 max 215586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215586 Ave neighs/atom = 172.88372 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.584 | 5.584 | 5.584 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 -4173.6509 -4173.6509 35.77021 83.420923 6.9938236 29.350298 29.350298 34.35201 26.760807 26.938076 2.5361495 1141.9069 Loop time of 2.156e-06 on 1 procs for 0 steps with 1247 atoms 185.5% 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 | | 2.156e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6204.00 ave 6204 max 6204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107793.0 ave 107793 max 107793 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 215586.0 ave 215586 max 215586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215586 Ave neighs/atom = 172.88372 Neighbor list builds = 0 Dangerous builds = 0 1247 -4097.29241956548 eV 2.53614948738414 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01