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 -59.934596 0.0000000) to (48.936393 59.934596 9.9204450) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0332539 5.7471531 6.6136300 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -59.934596 0.0000000) to (48.936393 59.934596 9.9204450) create_atoms CPU = 0.007 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0332539 5.7471531 6.6136300 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -59.934596 0.0000000) to (48.936393 59.934596 9.9204450) create_atoms CPU = 0.006 seconds 1755 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 = 12 29 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 3491 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 = 12 29 3 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) = 6.586 | 6.586 | 6.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11556.017 0 -11556.017 1394.3348 88 0 -11699.014 0 -11699.014 651.04097 Loop time of 7.4929 on 1 procs for 88 steps with 3491 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 = -11556.0170995943 -11699.0033315856 -11699.0141783926 Force two-norm initial, final = 68.026441 0.28814101 Force max component initial, final = 8.2299313 0.084012760 Final line search alpha, max atom move = 1.0000000 0.084012760 Iterations, force evaluations = 88 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1714 | 7.1714 | 7.1714 | 0.0 | 95.71 Neigh | 0.22833 | 0.22833 | 0.22833 | 0.0 | 3.05 Comm | 0.039684 | 0.039684 | 0.039684 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05352 | | | 0.71 Nlocal: 3491.00 ave 3491 max 3491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10707.0 ave 10707 max 10707 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: 486242.0 ave 486242 max 486242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 486242 Ave neighs/atom = 139.28445 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 12 29 3 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 : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.586 | 6.586 | 6.586 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -11699.014 0 -11699.014 651.04097 58192.992 93 0 -11699.3 0 -11699.3 62.137696 58235.06 Loop time of 0.341124 on 1 procs for 5 steps with 3491 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 = -11699.0141783926 -11699.2969136779 -11699.2996787634 Force two-norm initial, final = 116.61497 3.9772891 Force max component initial, final = 112.60304 2.6126190 Final line search alpha, max atom move = 0.00012240441 0.00031979609 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33222 | 0.33222 | 0.33222 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016559 | 0.0016559 | 0.0016559 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007253 | | | 2.13 Nlocal: 3491.00 ave 3491 max 3491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10683.0 ave 10683 max 10683 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: 486580.0 ave 486580 max 486580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 486580 Ave neighs/atom = 139.38127 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 = 12 30 3 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) = 6.725 | 6.725 | 6.725 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11699.3 0 -11699.3 62.137696 Loop time of 6.465e-06 on 1 procs for 0 steps with 3491 atoms 185.6% 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 | | 6.465e-06 | | |100.00 Nlocal: 3491.00 ave 3491 max 3491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10699.0 ave 10699 max 10699 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: 486430.0 ave 486430 max 486430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 486430 Ave neighs/atom = 139.33830 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 = 12 30 3 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) = 6.725 | 6.725 | 6.725 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 -11699.3 -11699.3 48.853017 120.39283 9.9013067 62.137696 62.137696 49.194071 72.192976 65.026042 2.5699808 2305.2987 Loop time of 7.638e-06 on 1 procs for 0 steps with 3491 atoms 261.8% 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 | | 7.638e-06 | | |100.00 Nlocal: 3491.00 ave 3491 max 3491 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10699.0 ave 10699 max 10699 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243215.0 ave 243215 max 243215 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 486430.0 ave 486430 max 486430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 486430 Ave neighs/atom = 139.33830 Neighbor list builds = 0 Dangerous builds = 0 3491 -11699.2996791272 eV 2.56998079662287 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09