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 = 3.61105 3.61105 3.61105 Created orthogonal box = (0 -69.0871 0) to (39.8854 69.0871 6.25452) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.88473 5.28507 6.25452 Created 1466 atoms create_atoms CPU = 0.000838995 secs 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.88473 5.28507 6.25452 Created 1466 atoms create_atoms CPU = 0.000749111 secs 1466 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 27 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2906 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 13.3 | 13.3 | 13.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11922.254 0 -11922.254 5169.6303 114 0 -12030.979 0 -12030.979 -8152.6153 Loop time of 4.40045 on 1 procs for 114 steps with 2906 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 = -11922.2538075 -12030.9671892 -12030.9789599 Force two-norm initial, final = 79.4164 0.448506 Force max component initial, final = 19.1357 0.0707077 Final line search alpha, max atom move = 0.651075 0.0460361 Iterations, force evaluations = 114 203 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2829 | 4.2829 | 4.2829 | 0.0 | 97.33 Neigh | 0.081184 | 0.081184 | 0.081184 | 0.0 | 1.84 Comm | 0.023535 | 0.023535 | 0.023535 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01282 | | | 0.29 Nlocal: 2906 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19015 ave 19015 max 19015 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: 1.10218e+06 ave 1.10218e+06 max 1.10218e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1102184 Ave neighs/atom = 379.279 Neighbor list builds = 4 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 : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.3 | 13.3 | 13.3 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -12030.979 0 -12030.979 -8152.6153 34469.471 117 0 -12031.08 0 -12031.08 -5248.7419 34410.249 Loop time of 0.123188 on 1 procs for 3 steps with 2906 atoms 97.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12030.9789599 -12031.0798391 -12031.0804077 Force two-norm initial, final = 122.398 0.493573 Force max component initial, final = 119.172 0.0710241 Final line search alpha, max atom move = 0.00010365 7.36163e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12117 | 0.12117 | 0.12117 | 0.0 | 98.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055432 | 0.00055432 | 0.00055432 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001461 | | | 1.19 Nlocal: 2906 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19020 ave 19020 max 19020 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: 1.10254e+06 ave 1.10254e+06 max 1.10254e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1102536 Ave neighs/atom = 379.4 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 12.82 | 12.82 | 12.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12031.08 0 -12031.08 -5248.7419 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2906 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: 2906 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19042 ave 19042 max 19042 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: 1.10284e+06 ave 1.10284e+06 max 1.10284e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1102844 Ave neighs/atom = 379.506 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) = 12.82 | 12.82 | 12.82 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 -12031.08 -12031.08 39.81789 138.17417 6.2543578 -5248.7419 -5248.7419 -3.1504952 -15740.955 -2.1204991 2.3118314 1213.1907 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2906 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 | | 2.146e-06 | | |100.00 Nlocal: 2906 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19042 ave 19042 max 19042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 551422 ave 551422 max 551422 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.10284e+06 ave 1.10284e+06 max 1.10284e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1102844 Ave neighs/atom = 379.506 Neighbor list builds = 0 Dangerous builds = 0 2906 -12031.0804076971 eV 2.31183135091335 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04