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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -36.865913 0.0000000) to (31.926817 36.865913 6.2613639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7304543 5.6716789 6.2613639 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -36.865913 0.0000000) to (31.926817 36.865913 6.2613639) create_atoms CPU = 0.004 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7304543 5.6716789 6.2613639 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -36.865913 0.0000000) to (31.926817 36.865913 6.2613639) create_atoms CPU = 0.003 seconds 630 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 20 2 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1252 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.445 | 5.445 | 5.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4228.3309 0 -4228.3309 23152.795 88 0 -4408.8131 0 -4408.8131 12450.224 Loop time of 3.08528 on 1 procs for 88 steps with 1252 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 = -4228.33089785882 -4408.80940413546 -4408.81313595841 Force two-norm initial, final = 78.733711 0.19208276 Force max component initial, final = 10.858547 0.041315599 Final line search alpha, max atom move = 1.0000000 0.041315599 Iterations, force evaluations = 88 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9558 | 2.9558 | 2.9558 | 0.0 | 95.80 Neigh | 0.082531 | 0.082531 | 0.082531 | 0.0 | 2.67 Comm | 0.02356 | 0.02356 | 0.02356 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02342 | | | 0.76 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6215.00 ave 6215 max 6215 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: 210100.0 ave 210100 max 210100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210100 Ave neighs/atom = 167.81150 Neighbor list builds = 3 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.445 | 5.445 | 5.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -4408.8131 0 -4408.8131 12450.224 14739.392 97 0 -4409.6289 0 -4409.6289 -206.56788 14873.347 Loop time of 0.223014 on 1 procs for 9 steps with 1252 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4408.81313595841 -4409.62769349583 -4409.62890515482 Force two-norm initial, final = 218.07781 3.5447714 Force max component initial, final = 181.50572 2.7544968 Final line search alpha, max atom move = 0.00018399831 0.00050682276 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21576 | 0.21576 | 0.21576 | 0.0 | 96.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015446 | 0.0015446 | 0.0015446 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005713 | | | 2.56 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6215.00 ave 6215 max 6215 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: 211528.0 ave 211528 max 211528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211528 Ave neighs/atom = 168.95208 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.583 | 5.583 | 5.583 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4409.6289 0 -4409.6289 -206.56788 Loop time of 8.67e-06 on 1 procs for 0 steps with 1252 atoms 173.0% 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 | | 8.67e-06 | | |100.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6212.00 ave 6212 max 6212 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: 205400.0 ave 205400 max 205400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205400 Ave neighs/atom = 164.05751 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.583 | 5.583 | 5.583 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 -4409.6289 -4409.6289 31.987034 74.351225 6.2538378 -206.56788 -206.56788 -297.27765 -117.26754 -205.15844 2.3152775 902.27581 Loop time of 8.7e-06 on 1 procs for 0 steps with 1252 atoms 218.4% 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 | | 8.7e-06 | | |100.00 Nlocal: 1252.00 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6212.00 ave 6212 max 6212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102700.0 ave 102700 max 102700 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205400.0 ave 205400 max 205400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205400 Ave neighs/atom = 164.05751 Neighbor list builds = 0 Dangerous builds = 0 1252 -4409.62890515482 eV 2.31527750122409 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03