LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.12887 4.12887 4.12887 Created orthogonal box = (0 -53.5204 0) to (30.8976 53.5204 7.15142) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.62092 6.37099 7.15142 Created 676 atoms create_atoms CPU = 0.000491142 secs 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.62092 6.37099 7.15142 Created 676 atoms create_atoms CPU = 0.000396013 secs 676 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 24 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1332 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.504 | 5.504 | 5.504 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4915.4509 0 -4915.4509 -3793.0933 50 0 -4934.949 0 -4934.949 -6389.4551 Loop time of 0.823805 on 1 procs for 50 steps with 1332 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4915.4509489 -4934.94458119 -4934.94897415 Force two-norm initial, final = 25.3954 0.153765 Force max component initial, final = 4.84997 0.0157668 Final line search alpha, max atom move = 1 0.0157668 Iterations, force evaluations = 50 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8103 | 0.8103 | 0.8103 | 0.0 | 98.36 Neigh | 0.0052969 | 0.0052969 | 0.0052969 | 0.0 | 0.64 Comm | 0.0050673 | 0.0050673 | 0.0050673 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003139 | | | 0.38 Nlocal: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7778 ave 7778 max 7778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235720 ave 235720 max 235720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235720 Ave neighs/atom = 176.967 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) 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) = 5.504 | 5.504 | 5.504 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -4934.949 0 -4934.949 -6389.4551 23651.945 54 0 -4935.2086 0 -4935.2086 -579.10055 23515.539 Loop time of 0.0613589 on 1 procs for 4 steps with 1332 atoms 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4934.94897415 -4935.20511092 -4935.20856954 Force two-norm initial, final = 127.673 7.04037 Force max component initial, final = 98.9642 7.03745 Final line search alpha, max atom move = 8.33849e-05 0.000586817 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060126 | 0.060126 | 0.060126 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029087 | 0.00029087 | 0.00029087 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000942 | | | 1.54 Nlocal: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7775 ave 7775 max 7775 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235752 ave 235752 max 235752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235752 Ave neighs/atom = 176.991 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.642 | 5.642 | 5.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4935.2086 0 -4935.2086 -579.10055 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1332 atoms 0.0% 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 | | 1.192e-06 | | |100.00 Nlocal: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7778 ave 7778 max 7778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 239152 ave 239152 max 239152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239152 Ave neighs/atom = 179.544 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.642 | 5.642 | 5.642 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 -4935.2086 -4935.2086 30.829656 107.04084 7.1258512 -579.10055 -579.10055 478.42527 -2209.5883 -6.1386516 2.6828571 1052.4066 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1332 atoms 0.0% 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 | | 1.907e-06 | | |100.00 Nlocal: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7778 ave 7778 max 7778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119576 ave 119576 max 119576 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 239152 ave 239152 max 239152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239152 Ave neighs/atom = 179.544 Neighbor list builds = 0 Dangerous builds = 0 1332 -4935.2085695396 eV 2.68285714042882 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01