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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -59.934678 0.0000000) to (48.936460 59.934678 9.9204585) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0332622 5.7471609 6.6136390 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -59.934678 0.0000000) to (48.936460 59.934678 9.9204585) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0332622 5.7471609 6.6136390 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -59.934678 0.0000000) to (48.936460 59.934678 9.9204585) create_atoms CPU = 0.002 seconds 1759 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 32 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3504 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_120808805541_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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 6.499 | 6.499 | 6.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10727.54 0 -10727.54 297256.4 81 0 -11844.119 0 -11844.119 3791.4778 Loop time of 2.73521 on 1 procs for 81 steps with 3504 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10727.5398712338 -11844.1084128344 -11844.1188941595 Force two-norm initial, final = 11172.064 0.25537391 Force max component initial, final = 1618.6578 0.068348615 Final line search alpha, max atom move = 1.0000000 0.068348615 Iterations, force evaluations = 81 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6332 | 2.6332 | 2.6332 | 0.0 | 96.27 Neigh | 0.063678 | 0.063678 | 0.063678 | 0.0 | 2.33 Comm | 0.015268 | 0.015268 | 0.015268 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02305 | | | 0.84 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9520.00 ave 9520 max 9520 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: 427790.0 ave 427790 max 427790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 427790 Ave neighs/atom = 122.08619 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.499 | 6.499 | 6.499 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -11844.119 0 -11844.119 3791.4778 58193.23 87 0 -11844.723 0 -11844.723 -241.39877 58496.903 Loop time of 0.140263 on 1 procs for 6 steps with 3504 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 = -11844.1188941594 -11844.7154391269 -11844.723013426 Force two-norm initial, final = 261.95093 16.474562 Force max component initial, final = 225.90717 13.377557 Final line search alpha, max atom move = 5.2940952e-05 0.00070822061 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13594 | 0.13594 | 0.13594 | 0.0 | 96.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056799 | 0.00056799 | 0.00056799 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003752 | | | 2.67 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9422.00 ave 9422 max 9422 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: 448106.0 ave 448106 max 448106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448106 Ave neighs/atom = 127.88413 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 6.637 | 6.637 | 6.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11844.723 0 -11844.723 -241.39877 Loop time of 1.902e-06 on 1 procs for 0 steps with 3504 atoms 157.7% 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 | | 1.902e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9427.00 ave 9427 max 9427 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: 430090.0 ave 430090 max 430090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 430090 Ave neighs/atom = 122.74258 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 6.637 | 6.637 | 6.637 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 -11844.723 -11844.723 48.914691 120.55164 9.9202006 -241.39877 -241.39877 -366.23603 -127.2574 -230.70288 2.5743398 1969.6681 Loop time of 2.441e-06 on 1 procs for 0 steps with 3504 atoms 163.9% 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 | | 2.441e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9427.00 ave 9427 max 9427 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 215045.0 ave 215045 max 215045 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 430090.0 ave 430090 max 430090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 430090 Ave neighs/atom = 122.74258 Neighbor list builds = 0 Dangerous builds = 0 3504 -11844.723013426 eV 2.57433980232933 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03