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 = 4.0500047 4.0500047 4.0500047 Created orthogonal box = (0.0000000 -76.415336 0.0000000) to (38.207668 76.415336 4.0500047) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5808953 5.5808953 4.0500047 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -76.415336 0.0000000) to (38.207668 76.415336 4.0500047) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5808953 5.5808953 4.0500047 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -76.415336 0.0000000) to (38.207668 76.415336 4.0500047) create_atoms CPU = 0.002 seconds 714 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 37 1 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1426 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_651801486679_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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 37 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.509 | 5.509 | 5.509 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4732.3002 0 -4732.3002 3953.8924 69 0 -4782.0241 0 -4782.0241 3664.8241 Loop time of 3.0122 on 1 procs for 69 steps with 1426 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4732.30023513818 -4782.02052484082 -4782.02406233316 Force two-norm initial, final = 23.246875 0.14918707 Force max component initial, final = 3.4170547 0.027002917 Final line search alpha, max atom move = 1.0000000 0.027002917 Iterations, force evaluations = 69 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9598 | 2.9598 | 2.9598 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.02972 | 0.02972 | 0.02972 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02272 | | | 0.75 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9894.00 ave 9894 max 9894 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: 200256.0 ave 200256 max 200256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200256 Ave neighs/atom = 140.43198 Neighbor list builds = 0 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 37 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.517 | 5.517 | 5.517 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -4782.0241 0 -4782.0241 3664.8241 23649.207 78 0 -4782.4184 0 -4782.4184 26.017936 23758.001 Loop time of 0.314589 on 1 procs for 9 steps with 1426 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 = -4782.02406233316 -4782.41834367367 -4782.41837204302 Force two-norm initial, final = 116.91406 0.78392386 Force max component initial, final = 110.84536 0.60574876 Final line search alpha, max atom move = 0.0012974495 0.00078592844 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27318 | 0.27318 | 0.27318 | 0.0 | 86.84 Neigh | 0.027717 | 0.027717 | 0.027717 | 0.0 | 8.81 Comm | 0.0038674 | 0.0038674 | 0.0038674 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009824 | | | 3.12 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11003.0 ave 11003 max 11003 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: 198952.0 ave 198952 max 198952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198952 Ave neighs/atom = 139.51753 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 38 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.656 | 5.656 | 5.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4782.4184 0 -4782.4184 26.017936 Loop time of 6.455e-06 on 1 procs for 0 steps with 1426 atoms 216.9% 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 | | 6.455e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11003.0 ave 11003 max 11003 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: 198940.0 ave 198940 max 198940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198940 Ave neighs/atom = 139.50912 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 38 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.656 | 5.656 | 5.656 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 -4782.4184 -4782.4184 38.135777 154.03566 4.0444179 26.017936 26.017936 40.773224 23.897531 13.383053 2.5801992 607.75185 Loop time of 1.0114e-05 on 1 procs for 0 steps with 1426 atoms 405.4% 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 | | 1.011e-05 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11003.0 ave 11003 max 11003 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99470.0 ave 99470 max 99470 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 198940.0 ave 198940 max 198940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198940 Ave neighs/atom = 139.50912 Neighbor list builds = 0 Dangerous builds = 0 1426 -4782.41837219164 eV 2.58019920082133 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04