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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009647 41.649202 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296739 5.3548974 5.7481360 Created 1664 atoms using lattice units in orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009647 41.649202 8.6222040) create_atoms CPU = 0.003 seconds 1664 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296739 5.3548974 5.7481360 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009647 41.649202 8.6222040) create_atoms CPU = 0.003 seconds 1688 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3352 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_101214310689_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 8.284 | 8.284 | 8.284 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14726.337 0 -14726.337 7007.7994 73 0 -14847.077 0 -14847.077 3765.0994 Loop time of 5.6644 on 1 procs for 73 steps with 3352 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14726.3366293341 -14847.0639413346 -14847.0771765774 Force two-norm initial, final = 47.548568 0.39026323 Force max component initial, final = 3.9713472 0.045706047 Final line search alpha, max atom move = 1.0000000 0.045706047 Iterations, force evaluations = 73 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3513 | 5.3513 | 5.3513 | 0.0 | 94.47 Neigh | 0.25859 | 0.25859 | 0.25859 | 0.0 | 4.57 Comm | 0.025729 | 0.025729 | 0.025729 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02875 | | | 0.51 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13362.0 ave 13362 max 13362 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: 828840.0 ave 828840 max 828840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 828840 Ave neighs/atom = 247.26730 Neighbor list builds = 5 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.04 | 12.04 | 12.04 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -14847.077 0 -14847.077 3765.0994 36635.936 76 0 -14847.245 0 -14847.245 154.6732 36711.064 Loop time of 0.251855 on 1 procs for 3 steps with 3352 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 = -14847.0771765774 -14847.2379030934 -14847.2446535358 Force two-norm initial, final = 169.45079 7.6929916 Force max component initial, final = 151.54245 7.1982821 Final line search alpha, max atom move = 3.7556428e-05 0.00027034176 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24786 | 0.24786 | 0.24786 | 0.0 | 98.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056162 | 0.00056162 | 0.00056162 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00343 | | | 1.36 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13367.0 ave 13367 max 13367 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: 828952.0 ave 828952 max 828952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 828952 Ave neighs/atom = 247.30072 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 11.55 | 11.55 | 11.55 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14847.245 0 -14847.245 154.6732 Loop time of 2.509e-06 on 1 procs for 0 steps with 3352 atoms 199.3% 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 | | 2.509e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13367.0 ave 13367 max 13367 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: 828246.0 ave 828246 max 828246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 828246 Ave neighs/atom = 247.09010 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 11.55 | 11.55 | 11.55 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 -14847.245 -14847.245 51.0146 83.4761 8.6206564 154.6732 154.6732 110.18375 314.82391 39.01193 2.1988039 1753.7515 Loop time of 2.546e-06 on 1 procs for 0 steps with 3352 atoms 274.9% 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 | | 2.546e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13367.0 ave 13367 max 13367 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 414123.0 ave 414123 max 414123 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 828246.0 ave 828246 max 828246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 828246 Ave neighs/atom = 247.09010 Neighbor list builds = 0 Dangerous builds = 0 3352 -14771.6582262193 eV 2.19880394142154 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06