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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -62.312674 0.0000000) to (50.878085 62.312674 10.314067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2726407 5.9751879 6.8760448 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -62.312674 0.0000000) to (50.878085 62.312674 10.314067) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2726407 5.9751879 6.8760448 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -62.312674 0.0000000) to (50.878085 62.312674 10.314067) create_atoms CPU = 0.002 seconds 1759 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 12 28 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 3487 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_878712978062_003#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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 7.396 | 7.396 | 7.396 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12615.261 0 -12615.261 23893.222 83 0 -12981.049 0 -12981.049 422.49704 Loop time of 5.77694 on 1 procs for 83 steps with 3487 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 = -12615.2611062349 -12981.03715075 -12981.0488550108 Force two-norm initial, final = 615.40768 0.21740703 Force max component initial, final = 100.62110 0.035995392 Final line search alpha, max atom move = 1.0000000 0.035995392 Iterations, force evaluations = 83 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5933 | 5.5933 | 5.5933 | 0.0 | 96.82 Neigh | 0.13984 | 0.13984 | 0.13984 | 0.0 | 2.42 Comm | 0.018107 | 0.018107 | 0.018107 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02566 | | | 0.44 Nlocal: 3487.00 ave 3487 max 3487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11344.0 ave 11344 max 11344 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: 600612.0 ave 600612 max 600612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 600612 Ave neighs/atom = 172.24319 Neighbor list builds = 4 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.396 | 7.396 | 7.396 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -12981.049 0 -12981.049 422.49704 65398.397 86 0 -12981.116 0 -12981.116 -128.43708 65487.478 Loop time of 0.153943 on 1 procs for 3 steps with 3487 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12981.0488550107 -12981.1073911754 -12981.116285237 Force two-norm initial, final = 45.075885 10.020202 Force max component initial, final = 44.631687 7.7780803 Final line search alpha, max atom move = 7.6051936e-05 0.00059153807 Iterations, force evaluations = 3 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15154 | 0.15154 | 0.15154 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033737 | 0.00033737 | 0.00033737 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002065 | | | 1.34 Nlocal: 3487.00 ave 3487 max 3487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11342.0 ave 11342 max 11342 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: 603506.0 ave 603506 max 603506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603506 Ave neighs/atom = 173.07313 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 7.534 | 7.534 | 7.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12981.116 0 -12981.116 -128.43708 Loop time of 2.185e-06 on 1 procs for 0 steps with 3487 atoms 183.1% 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 | | 2.185e-06 | | |100.00 Nlocal: 3487.00 ave 3487 max 3487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11342.0 ave 11342 max 11342 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: 602892.0 ave 602892 max 602892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 602892 Ave neighs/atom = 172.89705 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 7.534 | 7.534 | 7.534 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 -12981.116 -12981.116 50.852579 124.99922 10.302389 -128.43708 -128.43708 -146.52522 -48.707748 -190.07829 2.7100127 2832.5241 Loop time of 2.199e-06 on 1 procs for 0 steps with 3487 atoms 227.4% 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 | | 2.199e-06 | | |100.00 Nlocal: 3487.00 ave 3487 max 3487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11342.0 ave 11342 max 11342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 301446.0 ave 301446 max 301446 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 602892.0 ave 602892 max 602892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 602892 Ave neighs/atom = 172.89705 Neighbor list builds = 0 Dangerous builds = 0 3487 -12981.116285237 eV 2.71001268472783 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07