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 = 3.6390875 3.6390875 3.6390875 Created orthogonal box = (0.0000000 -44.121591 0.0000000) to (36.025128 44.121591 8.9139075) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1464469 5.1024969 5.9426050 Created 1175 atoms using lattice units in orthogonal box = (0.0000000 -44.121591 0.0000000) to (36.025128 44.121591 8.9139075) create_atoms CPU = 0.001 seconds 1175 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1464469 5.1024969 5.9426050 Created 1183 atoms using lattice units in orthogonal box = (0.0000000 -44.121591 0.0000000) to (36.025128 44.121591 8.9139075) create_atoms CPU = 0.001 seconds 1183 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 ghost atom cutoff = 8 binsize = 4, bins = 10 23 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2336 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_945691923444_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 ghost atom cutoff = 8 binsize = 4, bins = 10 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.429 | 6.429 | 6.429 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6745.9632 0 -6745.9632 88899.598 80 0 -7628.7692 0 -7628.7692 -1892.4028 Loop time of 3.06895 on 1 procs for 80 steps with 2336 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6745.96315955884 -7628.7639302551 -7628.76922590855 Force two-norm initial, final = 1318.0155 0.17944884 Force max component initial, final = 229.39830 0.0080674368 Final line search alpha, max atom move = 1.0000000 0.0080674368 Iterations, force evaluations = 80 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9878 | 2.9878 | 2.9878 | 0.0 | 97.36 Neigh | 0.049474 | 0.049474 | 0.049474 | 0.0 | 1.61 Comm | 0.013221 | 0.013221 | 0.013221 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01842 | | | 0.60 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8834.00 ave 8834 max 8834 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: 409300.0 ave 409300 max 409300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409300 Ave neighs/atom = 175.21404 Neighbor list builds = 2 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 ghost atom cutoff = 8 binsize = 4, bins = 10 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.429 | 6.429 | 6.429 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -7628.7692 0 -7628.7692 -1892.4028 28337.062 83 0 -7628.8452 0 -7628.8452 230.06801 28295.602 Loop time of 0.103836 on 1 procs for 3 steps with 2336 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 = -7628.76922590852 -7628.84276107909 -7628.84515334769 Force two-norm initial, final = 75.184197 9.6267995 Force max component initial, final = 65.318010 9.2241129 Final line search alpha, max atom move = 8.9961123e-05 0.00082981155 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10138 | 0.10138 | 0.10138 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036082 | 0.00036082 | 0.00036082 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0021 | | | 2.02 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8592.00 ave 8592 max 8592 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: 408992.0 ave 408992 max 408992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 408992 Ave neighs/atom = 175.08219 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 ghost atom cutoff = 8 binsize = 4, bins = 9 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.566 | 6.566 | 6.566 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7628.8452 0 -7628.8452 230.06801 Loop time of 2.244e-06 on 1 procs for 0 steps with 2336 atoms 178.3% 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 | | 2.244e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8592.00 ave 8592 max 8592 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: 408976.0 ave 408976 max 408976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 408976 Ave neighs/atom = 175.07534 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 ghost atom cutoff = 8 binsize = 4, bins = 9 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.566 | 6.566 | 6.566 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 -7628.8452 -7628.8452 35.995213 88.340169 8.8984827 230.06801 230.06801 12.489165 522.86924 154.84561 2.2558812 1435.4684 Loop time of 3.056e-06 on 1 procs for 0 steps with 2336 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 | | 3.056e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8592.00 ave 8592 max 8592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 204488.0 ave 204488 max 204488 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 408976.0 ave 408976 max 408976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 408976 Ave neighs/atom = 175.07534 Neighbor list builds = 0 Dangerous builds = 0 2336 -7628.84515334769 eV 2.25588115288664 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03