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 -46.482005 0.0000000) to (37.952398 46.482005 7.6937562) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6790628 4.4571785 5.1291708 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -46.482005 0.0000000) to (37.952398 46.482005 7.6937562) create_atoms CPU = 0.002 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6790628 4.4571785 5.1291708 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -46.482005 0.0000000) to (37.952398 46.482005 7.6937562) create_atoms CPU = 0.001 seconds 878 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 = 7 17 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 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1754 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 = 7 17 2 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) = 7.608 | 7.608 | 7.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10517.552 0 -10517.552 123926.18 221 0 -11781.078 0 -11781.078 22305.673 Loop time of 13.4051 on 1 procs for 221 steps with 1754 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 = -10517.5521124374 -11781.0673556004 -11781.078337972 Force two-norm initial, final = 1548.7284 0.59696344 Force max component initial, final = 450.99594 0.083867700 Final line search alpha, max atom move = 1.0000000 0.083867700 Iterations, force evaluations = 221 421 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.1 | 13.1 | 13.1 | 0.0 | 97.72 Neigh | 0.20548 | 0.20548 | 0.20548 | 0.0 | 1.53 Comm | 0.058257 | 0.058257 | 0.058257 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04152 | | | 0.31 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12329.0 ave 12329 max 12329 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: 724528.0 ave 724528 max 724528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 724528 Ave neighs/atom = 413.07184 Neighbor list builds = 5 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 = 7 17 2 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 : 221 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.608 | 7.608 | 7.608 Mbytes Step Temp E_pair E_mol TotEng Press Volume 221 0 -11781.078 0 -11781.078 22305.673 27145.165 234 0 -11786.425 0 -11786.425 31.225006 27348.951 Loop time of 0.546023 on 1 procs for 13 steps with 1754 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 = -11781.078337972 -11786.4239123095 -11786.4245080165 Force two-norm initial, final = 966.90287 5.2529564 Force max component initial, final = 909.09296 2.1529961 Final line search alpha, max atom move = 0.00021558080 0.00046414462 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49713 | 0.49713 | 0.49713 | 0.0 | 91.04 Neigh | 0.038478 | 0.038478 | 0.038478 | 0.0 | 7.05 Comm | 0.0019694 | 0.0019694 | 0.0019694 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00845 | | | 1.55 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12365.0 ave 12365 max 12365 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: 718100.0 ave 718100 max 718100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 718100 Ave neighs/atom = 409.40707 Neighbor list builds = 1 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 = 7 17 2 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) = 7.747 | 7.747 | 7.747 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11786.425 0 -11786.425 31.225006 Loop time of 1.838e-06 on 1 procs for 0 steps with 1754 atoms 163.2% 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 | | 1.838e-06 | | |100.00 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12365.0 ave 12365 max 12365 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: 718132.0 ave 718132 max 718132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 718132 Ave neighs/atom = 409.42531 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 = 7 17 2 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) = 7.747 | 7.747 | 7.747 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 -11786.425 -11786.425 37.928746 94.054989 7.6663803 31.225006 31.225006 126.04981 73.847161 -106.22195 2.5707294 9535.1929 Loop time of 2.726e-06 on 1 procs for 0 steps with 1754 atoms 293.5% 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 | | 2.726e-06 | | |100.00 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12365.0 ave 12365 max 12365 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 359066.0 ave 359066 max 359066 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 718132.0 ave 718132 max 718132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 718132 Ave neighs/atom = 409.42531 Neighbor list builds = 0 Dangerous builds = 0 1754 -11786.4245080165 eV 2.57072939853328 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14