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 = 3.6583664 3.6583664 3.6583664 Created orthogonal box = (0.0000000 -41.389691 0.0000000) to (6.3364764 41.389691 8.9611309) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3364764 5.1737114 5.9740873 Created 192 atoms using lattice units in orthogonal box = (0.0000000 -41.389691 0.0000000) to (6.3364764 41.389691 8.9611309) create_atoms CPU = 0.001 seconds 192 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3364764 5.1737114 5.9740873 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -41.389691 0.0000000) to (6.3364764 41.389691 8.9611309) create_atoms CPU = 0.000 seconds 198 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 390 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_807997826449_000#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1342.747 0 -1342.747 194372.92 148 0 -1566.0246 0 -1566.0246 -3376.6555 Loop time of 0.950743 on 1 procs for 148 steps with 390 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1342.7469635118 -1566.02318133832 -1566.02460961103 Force two-norm initial, final = 280.26811 0.11916467 Force max component initial, final = 39.504484 0.010307454 Final line search alpha, max atom move = 1.0000000 0.010307454 Iterations, force evaluations = 148 288 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92698 | 0.92698 | 0.92698 | 0.0 | 97.50 Neigh | 0.0070128 | 0.0070128 | 0.0070128 | 0.0 | 0.74 Comm | 0.0093719 | 0.0093719 | 0.0093719 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007381 | | | 0.78 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3620.00 ave 3620 max 3620 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: 54708.0 ave 54708 max 54708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54708 Ave neighs/atom = 140.27692 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 148 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press Volume 148 0 -1566.0246 0 -1566.0246 -3376.6555 4700.3784 192 0 -1570.485 0 -1570.485 -476.08157 4717.2292 Loop time of 0.159501 on 1 procs for 44 steps with 390 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1566.02460961103 -1570.48375653765 -1570.48504499894 Force two-norm initial, final = 162.21645 3.0267962 Force max component initial, final = 121.07918 2.2765667 Final line search alpha, max atom move = 0.00049626417 0.0011297785 Iterations, force evaluations = 44 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14437 | 0.14437 | 0.14437 | 0.0 | 90.52 Neigh | 0.0073172 | 0.0073172 | 0.0073172 | 0.0 | 4.59 Comm | 0.0015849 | 0.0015849 | 0.0015849 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006226 | | | 3.90 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3637.00 ave 3637 max 3637 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: 55152.0 ave 55152 max 55152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55152 Ave neighs/atom = 141.41538 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.654 | 4.654 | 4.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1570.485 0 -1570.485 -476.08157 Loop time of 1.565e-06 on 1 procs for 0 steps with 390 atoms 191.7% 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 | | 1.565e-06 | | |100.00 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3604.00 ave 3604 max 3604 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: 54420.0 ave 54420 max 54420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54420 Ave neighs/atom = 139.53846 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.654 | 4.654 | 4.654 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 -1570.485 -1570.485 6.3292223 79.959756 9.3210571 -476.08157 -476.08157 -301.80242 -746.88379 -379.55849 2.3604694 77.676 Loop time of 1.656e-06 on 1 procs for 0 steps with 390 atoms 181.2% 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 | | 1.656e-06 | | |100.00 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3604.00 ave 3604 max 3604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27210.0 ave 27210 max 27210 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54420.0 ave 54420 max 54420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54420 Ave neighs/atom = 139.53846 Neighbor list builds = 0 Dangerous builds = 0 390 -1570.48504499894 eV 2.36046939437659 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01