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 = 3.16926 3.16926 3.16926 Created orthogonal box = (0 -43.5733 0) to (11.8583 43.5733 7.76307) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.08212 4.84112 5.17538 Created 254 atoms create_atoms CPU = 0.000256062 secs 254 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.08212 4.84112 5.17538 Created 254 atoms create_atoms CPU = 0.000129938 secs 254 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 4 27 3 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 500 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 4 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5375.8109 0 -5375.8109 -2104.8132 41 0 -5403.0535 0 -5403.0535 -10302.197 Loop time of 9.10249 on 1 procs for 41 steps with 500 atoms 73.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5375.81094709 -5403.04945711 -5403.0535061 Force two-norm initial, final = 50.9165 0.223457 Force max component initial, final = 16.9107 0.0512894 Final line search alpha, max atom move = 1 0.0512894 Iterations, force evaluations = 41 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.0985 | 9.0985 | 9.0985 | 0.0 | 99.96 Neigh | 0.001348 | 0.001348 | 0.001348 | 0.0 | 0.01 Comm | 0.0015275 | 0.0015275 | 0.0015275 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001096 | | | 0.01 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2793 ave 2793 max 2793 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: 32152 ave 32152 max 32152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32152 Ave neighs/atom = 64.304 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -5403.0535 0 -5403.0535 -10302.197 8022.4148 44 0 -5403.1439 0 -5403.1439 -1496.2609 7995.0416 Loop time of 0.698926 on 1 procs for 3 steps with 500 atoms 65.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5403.0535061 -5403.14311045 -5403.14391197 Force two-norm initial, final = 72.6773 0.240749 Force max component initial, final = 56.8102 0.0350468 Final line search alpha, max atom move = 0.000305802 1.07174e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.69848 | 0.69848 | 0.69848 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.3937e-05 | 9.3937e-05 | 9.3937e-05 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000355 | | | 0.05 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2793 ave 2793 max 2793 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: 32140 ave 32140 max 32140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32140 Ave neighs/atom = 64.28 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 4 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.625 | 4.625 | 4.625 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5403.1439 0 -5403.1439 -1496.2609 Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 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: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2793 ave 2793 max 2793 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: 32144 ave 32144 max 32144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32144 Ave neighs/atom = 64.288 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) = 4.625 | 4.625 | 4.625 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 -5403.1439 -5403.1439 11.844275 87.14654 7.7457254 -1496.2609 -1496.2609 -2.1443257 -4489.347 2.7086106 2.4167031 379.47515 Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 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: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2793 ave 2793 max 2793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16072 ave 16072 max 16072 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32144 ave 32144 max 32144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32144 Ave neighs/atom = 64.288 Neighbor list builds = 0 Dangerous builds = 0 500 -2725.84106519213 eV 2.41670307176211 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10