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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -57.473145 0.0000000) to (33.182136 57.473145 4.9649236) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4573019 4.5749768 4.9649236 Created 804 atoms using lattice units in orthogonal box = (0.0000000 -57.473145 0.0000000) to (33.182136 57.473145 4.9649236) create_atoms CPU = 0.006 seconds 804 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4573019 4.5749768 4.9649236 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -57.473145 0.0000000) to (33.182136 57.473145 4.9649236) create_atoms CPU = 0.005 seconds 806 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 41 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1610 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_142799717516_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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.725 | 4.725 | 4.725 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6805.3745 0 -6805.3745 17205.995 53 0 -6920.6272 0 -6920.6272 8380.9037 Loop time of 0.818756 on 1 procs for 53 steps with 1610 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 = -6805.3744566896 -6920.62028013504 -6920.62716098261 Force two-norm initial, final = 102.34256 0.33266505 Force max component initial, final = 25.647233 0.086786704 Final line search alpha, max atom move = 0.65978000 0.057260132 Iterations, force evaluations = 53 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78542 | 0.78542 | 0.78542 | 0.0 | 95.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01603 | 0.01603 | 0.01603 | 0.0 | 1.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0173 | | | 2.11 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6322.00 ave 6322 max 6322 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: 94184.0 ave 94184 max 94184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94184 Ave neighs/atom = 58.499379 Neighbor list builds = 0 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -6920.6272 0 -6920.6272 8380.9037 18937.03 56 0 -6920.8613 0 -6920.8613 -0.81289547 19024.748 Loop time of 0.0520894 on 1 procs for 3 steps with 1610 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 = -6920.62716098261 -6920.86024600775 -6920.86132190435 Force two-norm initial, final = 172.50630 0.66767049 Force max component initial, final = 113.49490 0.40551108 Final line search alpha, max atom move = 0.00017837033 7.2331147e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.048155 | 0.048155 | 0.048155 | 0.0 | 92.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082433 | 0.00082433 | 0.00082433 | 0.0 | 1.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00311 | | | 5.97 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6297.00 ave 6297 max 6297 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: 98096.0 ave 98096 max 98096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98096 Ave neighs/atom = 60.929193 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.863 | 4.863 | 4.863 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6920.8613 0 -6920.8613 -0.81289547 Loop time of 6.365e-06 on 1 procs for 0 steps with 1610 atoms 188.5% 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 | | 6.365e-06 | | |100.00 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6297.00 ave 6297 max 6297 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: 96616.0 ave 96616 max 96616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96616 Ave neighs/atom = 60.009938 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.863 | 4.863 | 4.863 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 -6920.8613 -6920.8613 33.22537 115.18514 4.9711017 -0.81289547 -0.81289547 -33.816936 -2.8145168 34.192767 2.3093572 718.62956 Loop time of 6.856e-06 on 1 procs for 0 steps with 1610 atoms 262.5% 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 | | 6.856e-06 | | |100.00 Nlocal: 1610.00 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6297.00 ave 6297 max 6297 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48308.0 ave 48308 max 48308 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96616.0 ave 96616 max 96616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96616 Ave neighs/atom = 60.009938 Neighbor list builds = 0 Dangerous builds = 0 1610 -6920.86132190435 eV 2.30935724297897 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01