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 = 3.63552 3.63552 3.63552 Created orthogonal box = (0 -52.9376 0) to (26.467 52.9376 3.63552) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4944 4.4944 3.63552 Created 426 atoms create_atoms CPU = 0.000262022 secs 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4944 4.4944 3.63552 Created 426 atoms create_atoms CPU = 0.000130892 secs 426 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 9 36 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 840 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3420.4019 0 -3420.4019 2062.0464 46 0 -3433.5782 0 -3433.5782 -6086.7569 Loop time of 9.98415 on 1 procs for 46 steps with 840 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3420.40186625 -3433.57546754 -3433.5781892 Force two-norm initial, final = 26.1721 0.134847 Force max component initial, final = 6.85615 0.0185869 Final line search alpha, max atom move = 1 0.0185869 Iterations, force evaluations = 46 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.9777 | 9.9777 | 9.9777 | 0.0 | 99.94 Neigh | 0.0020218 | 0.0020218 | 0.0020218 | 0.0 | 0.02 Comm | 0.0026951 | 0.0026951 | 0.0026951 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00169 | | | 0.02 Nlocal: 840 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4556 ave 4556 max 4556 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: 64628 ave 64628 max 64628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64628 Ave neighs/atom = 76.9381 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -3433.5782 0 -3433.5782 -6086.7569 10187.46 49 0 -3433.6359 0 -3433.6359 -1310.3006 10152.81 Loop time of 0.705112 on 1 procs for 3 steps with 840 atoms 100.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3433.5781892 -3433.63570863 -3433.63590954 Force two-norm initial, final = 47.251 0.157245 Force max component initial, final = 35.6221 0.0204495 Final line search alpha, max atom move = 0.00112419 2.29891e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70442 | 0.70442 | 0.70442 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016332 | 0.00016332 | 0.00016332 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005279 | | | 0.07 Nlocal: 840 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4560 ave 4560 max 4560 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: 64712 ave 64712 max 64712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64712 Ave neighs/atom = 77.0381 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.686 | 4.686 | 4.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3433.6359 0 -3433.6359 -1310.3006 Loop time of 1.19209e-06 on 1 procs for 0 steps with 840 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: 840 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4564 ave 4564 max 4564 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: 64720 ave 64720 max 64720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64720 Ave neighs/atom = 77.0476 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) = 4.686 | 4.686 | 4.686 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 -3433.6359 -3433.6359 26.411984 105.87526 3.6307032 -1310.3006 -1310.3006 1.110007 -3929.1796 -2.8322372 2.3300665 360.49537 Loop time of 9.53674e-07 on 1 procs for 0 steps with 840 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: 840 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4564 ave 4564 max 4564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32360 ave 32360 max 32360 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 64720 ave 64720 max 64720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64720 Ave neighs/atom = 77.0476 Neighbor list builds = 0 Dangerous builds = 0 840 -2949.43355890512 eV 2.33006649543271 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11