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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -49.103641 0.0000000) to (40.092955 49.103641 9.9204336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7275650 5.6786524 6.6136224 Created 1175 atoms using lattice units in orthogonal box = (0.0000000 -49.103641 0.0000000) to (40.092955 49.103641 9.9204336) create_atoms CPU = 0.002 seconds 1175 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7275650 5.6786524 6.6136224 Created 1183 atoms using lattice units in orthogonal box = (0.0000000 -49.103641 0.0000000) to (40.092955 49.103641 9.9204336) create_atoms CPU = 0.002 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 24 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 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_751354403791_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 = 10 24 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) = 5.990 | 5.990 | 5.990 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7761.5231 0 -7761.5231 -37.632283 82 0 -7824.5465 0 -7824.5465 -1304.3475 Loop time of 2.6971 on 1 procs for 82 steps with 2336 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7761.52310227513 -7824.53900019643 -7824.54651746809 Force two-norm initial, final = 27.275298 0.21818675 Force max component initial, final = 3.3504612 0.054170355 Final line search alpha, max atom move = 1.0000000 0.054170355 Iterations, force evaluations = 82 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6139 | 2.6139 | 2.6139 | 0.0 | 96.92 Neigh | 0.049107 | 0.049107 | 0.049107 | 0.0 | 1.82 Comm | 0.013765 | 0.013765 | 0.013765 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02032 | | | 0.75 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7918.00 ave 7918 max 7918 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: 325716.0 ave 325716 max 325716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325716 Ave neighs/atom = 139.43322 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 24 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 : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.990 | 5.990 | 5.990 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -7824.5465 0 -7824.5465 -1304.3475 39060.916 85 0 -7824.5991 0 -7824.5991 2.792377 38995.92 Loop time of 0.0853605 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 = -7824.54651746808 -7824.59891088933 -7824.59910013328 Force two-norm initial, final = 61.677547 0.56721404 Force max component initial, final = 52.063112 0.33973212 Final line search alpha, max atom move = 0.00026204609 8.9025475e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.082806 | 0.082806 | 0.082806 | 0.0 | 97.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034439 | 0.00034439 | 0.00034439 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00221 | | | 2.59 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7905.00 ave 7905 max 7905 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: 325698.0 ave 325698 max 325698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325698 Ave neighs/atom = 139.42551 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 = 10 24 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) = 6.128 | 6.128 | 6.128 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7824.5991 0 -7824.5991 2.792377 Loop time of 2.372e-06 on 1 procs for 0 steps with 2336 atoms 168.6% 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 | | 2.372e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7905.00 ave 7905 max 7905 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: 325662.0 ave 325662 max 325662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325662 Ave neighs/atom = 139.41010 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 = 10 24 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) = 6.128 | 6.128 | 6.128 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 -7824.5991 -7824.5991 40.073137 98.280181 9.9014745 2.792377 2.792377 -13.951249 13.284046 9.0443338 2.574563 1777.6777 Loop time of 2.598e-06 on 1 procs for 0 steps with 2336 atoms 269.4% 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 | | 2.598e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7905.00 ave 7905 max 7905 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162831.0 ave 162831 max 162831 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 325662.0 ave 325662 max 325662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325662 Ave neighs/atom = 139.41010 Neighbor list builds = 0 Dangerous builds = 0 2336 -7824.59910003104 eV 2.57456302874943 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03