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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -43.246066 0.0000000) to (24.965789 43.246066 7.0147812) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5699446 6.0690548 7.0147812 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.246066 0.0000000) to (24.965789 43.246066 7.0147812) create_atoms CPU = 0.003 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5699446 6.0690548 7.0147812 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.246066 0.0000000) to (24.965789 43.246066 7.0147812) create_atoms CPU = 0.003 seconds 458 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 29 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 892 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_022920256108_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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 -2961.6286 0 -2961.6286 995.00803 50 0 -2976.821 0 -2976.821 -7731.7116 Loop time of 3.58361 on 1 procs for 50 steps with 892 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 = -2961.62855306554 -2976.82064544687 -2976.8209620979 Force two-norm initial, final = 16.775838 1.0233933 Force max component initial, final = 3.9843210 0.44558811 Final line search alpha, max atom move = 0.034042504 0.015168935 Iterations, force evaluations = 50 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5502 | 3.5502 | 3.5502 | 0.0 | 99.07 Neigh | 0.01218 | 0.01218 | 0.01218 | 0.0 | 0.34 Comm | 0.0089291 | 0.0089291 | 0.0089291 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01229 | | | 0.34 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3082.00 ave 3082 max 3082 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: 47604.0 ave 47604 max 47604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47604 Ave neighs/atom = 53.367713 Neighbor list builds = 1 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 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 50 0 -2976.821 0 -2976.821 -7731.7116 15147.328 56 0 -2977.0564 0 -2977.0564 -2602.0339 15023.402 Loop time of 0.287991 on 1 procs for 6 steps with 892 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2976.8209620979 -2977.055778064 -2977.05640738303 Force two-norm initial, final = 79.421408 0.85298935 Force max component initial, final = 60.517727 0.26376141 Final line search alpha, max atom move = 0.00045289629 0.00011945656 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28448 | 0.28448 | 0.28448 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063314 | 0.00063314 | 0.00063314 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002877 | | | 1.00 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3090.00 ave 3090 max 3090 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: 47640.0 ave 47640 max 47640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47640 Ave neighs/atom = 53.408072 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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 -2977.0564 0 -2977.0564 -2602.0339 Loop time of 6.635e-06 on 1 procs for 0 steps with 892 atoms 180.9% 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 | | 6.635e-06 | | |100.00 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3090.00 ave 3090 max 3090 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: 47664.0 ave 47664 max 47664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47664 Ave neighs/atom = 53.434978 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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 -2977.0564 -2977.0564 24.838554 86.492131 6.9930299 -2602.0339 -2602.0339 16.527177 -7800.6537 -21.975224 2.5664313 792.52088 Loop time of 6.825e-06 on 1 procs for 0 steps with 892 atoms 278.4% 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 | | 6.825e-06 | | |100.00 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3090.00 ave 3090 max 3090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23832.0 ave 23832 max 23832 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47664.0 ave 47664 max 47664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47664 Ave neighs/atom = 53.434978 Neighbor list builds = 0 Dangerous builds = 0 892 -2977.05640738303 eV 2.56643134892673 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04