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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -36.738953 0.0000000) to (18.369476 36.738953 2.8688302) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0323241 4.0323241 2.8688302 Created 164 atoms using lattice units in orthogonal box = (0.0000000 -36.738953 0.0000000) to (18.369476 36.738953 2.8688302) create_atoms CPU = 0.002 seconds 164 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0323241 4.0323241 2.8688302 Created 165 atoms using lattice units in orthogonal box = (0.0000000 -36.738953 0.0000000) to (18.369476 36.738953 2.8688302) create_atoms CPU = 0.001 seconds 165 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 15 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 325 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 4.882 | 4.882 | 4.882 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1233.7022 0 -1233.7022 45493.328 99 0 -1336.9164 0 -1336.9164 -10475.843 Loop time of 3.17272 on 1 procs for 99 steps with 325 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 = -1233.7022014901 -1336.91503102046 -1336.91636556919 Force two-norm initial, final = 250.07656 0.15887813 Force max component initial, final = 120.34672 0.031474381 Final line search alpha, max atom move = 1.0000000 0.031474381 Iterations, force evaluations = 99 180 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0972 | 3.0972 | 3.0972 | 0.0 | 97.62 Neigh | 0.029456 | 0.029456 | 0.029456 | 0.0 | 0.93 Comm | 0.030962 | 0.030962 | 0.030962 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01514 | | | 0.48 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6731.00 ave 6731 max 6731 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: 123550.0 ave 123550 max 123550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123550 Ave neighs/atom = 380.15385 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.882 | 4.882 | 4.882 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -1336.9164 0 -1336.9164 -10475.843 3872.2055 171 0 -1339.0958 0 -1339.0958 -181.19119 3843.485 Loop time of 1.47735 on 1 procs for 72 steps with 325 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 = -1336.91636556919 -1339.09449195651 -1339.09576332012 Force two-norm initial, final = 76.529296 1.7579239 Force max component initial, final = 72.483353 1.1129475 Final line search alpha, max atom move = 0.00023846069 0.00026539423 Iterations, force evaluations = 72 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4155 | 1.4155 | 1.4155 | 0.0 | 95.82 Neigh | 0.014425 | 0.014425 | 0.014425 | 0.0 | 0.98 Comm | 0.012289 | 0.012289 | 0.012289 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03511 | | | 2.38 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6619.00 ave 6619 max 6619 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: 121932.0 ave 121932 max 121932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121932 Ave neighs/atom = 375.17538 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.026 | 5.026 | 5.026 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1339.0958 0 -1339.0958 -181.19119 Loop time of 9.682e-06 on 1 procs for 0 steps with 325 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 | | 9.682e-06 | | |100.00 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7469.00 ave 7469 max 7469 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: 122026.0 ave 122026 max 122026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122026 Ave neighs/atom = 375.46462 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.026 | 5.026 | 5.026 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 -1339.0958 -1339.0958 18.788324 74.870104 2.7323021 -181.19119 -181.19119 -152.91286 51.198303 -441.85901 2.3185134 141.97537 Loop time of 1.1216e-05 on 1 procs for 0 steps with 325 atoms 222.9% 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 | | 1.122e-05 | | |100.00 Nlocal: 325.000 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7469.00 ave 7469 max 7469 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61013.0 ave 61013 max 61013 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 122026.0 ave 122026 max 122026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122026 Ave neighs/atom = 375.46462 Neighbor list builds = 0 Dangerous builds = 0 325 -1339.09576332012 eV 2.31851336405645 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05