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 = 3.63376 3.63376 3.63376 Created orthogonal box = (0 -37.0609 0) to (18.5286 37.0609 3.63376) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.27584 4.27584 3.63376 Created 210 atoms create_atoms CPU = 0.000200033 secs 210 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.27584 4.27584 3.63376 Created 210 atoms create_atoms CPU = 6.38962e-05 secs 210 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 25 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 412 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1672.7572 0 -1672.7572 2340.0077 17 0 -1681.7492 0 -1681.7492 -7978.771 Loop time of 6.6531 on 1 procs for 17 steps with 412 atoms 80.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1672.75718084 -1681.74783163 -1681.74924187 Force two-norm initial, final = 18.0579 0.101766 Force max component initial, final = 6.13793 0.022306 Final line search alpha, max atom move = 1 0.022306 Iterations, force evaluations = 17 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.652 | 6.652 | 6.652 | 0.0 | 99.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066471 | 0.00066471 | 0.00066471 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003886 | | | 0.01 Nlocal: 412 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3212 ave 3212 max 3212 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: 31856 ave 31856 max 31856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31856 Ave neighs/atom = 77.3204 Neighbor list builds = 0 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 : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -1681.7492 0 -1681.7492 -7978.771 4990.5134 20 0 -1681.7975 0 -1681.7975 -1611.847 4967.9696 Loop time of 1.36613 on 1 procs for 3 steps with 412 atoms 65.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1681.74924187 -1681.79652321 -1681.79750332 Force two-norm initial, final = 30.1777 0.82182 Force max component initial, final = 21.7013 0.677293 Final line search alpha, max atom move = 0.000281774 0.000190844 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3657 | 1.3657 | 1.3657 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.9884e-05 | 8.9884e-05 | 8.9884e-05 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002904 | | | 0.02 Nlocal: 412 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3182 ave 3182 max 3182 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: 32008 ave 32008 max 32008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32008 Ave neighs/atom = 77.6893 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1681.7975 0 -1681.7975 -1611.847 Loop time of 9.53674e-07 on 1 procs for 0 steps with 412 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 | | 9.537e-07 | | |100.00 Nlocal: 412 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3182 ave 3182 max 3182 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: 32016 ave 32016 max 32016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32016 Ave neighs/atom = 77.7087 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) = 4.586 | 4.586 | 4.586 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 -1681.7975 -1681.7975 18.48905 74.121753 3.6250889 -1611.847 -1611.847 217.96143 -4909.5009 -144.00161 2.3215525 191.94786 Loop time of 9.53674e-07 on 1 procs for 0 steps with 412 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 | | 9.537e-07 | | |100.00 Nlocal: 412 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3182 ave 3182 max 3182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16008 ave 16008 max 16008 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32016 ave 32016 max 32016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32016 Ave neighs/atom = 77.7087 Neighbor list builds = 0 Dangerous builds = 0 412 -631.559516361209 eV 2.32155245547961 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09