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 = 3.65334 3.65334 3.65334 Created orthogonal box = (0 -63.2814 0) to (25.833 63.2814 8.94883) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.19993 5.48407 5.96589 Created 1204 atoms create_atoms CPU = 0.000629902 secs 1204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.19993 5.48407 5.96589 Created 1204 atoms create_atoms CPU = 0.00051403 secs 1204 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 6 29 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2384 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 6 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.95 | 6.95 | 6.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7723.8111 0 -7723.8111 1988.0864 44 0 -7781.6304 0 -7781.6304 -8734.1243 Loop time of 0.779899 on 1 procs for 44 steps with 2384 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 = -7723.8110931 -7781.62292217 -7781.6303625 Force two-norm initial, final = 38.3398 0.319252 Force max component initial, final = 6.50627 0.0267892 Final line search alpha, max atom move = 1 0.0267892 Iterations, force evaluations = 44 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75316 | 0.75316 | 0.75316 | 0.0 | 96.57 Neigh | 0.01613 | 0.01613 | 0.01613 | 0.0 | 2.07 Comm | 0.0059373 | 0.0059373 | 0.0059373 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00467 | | | 0.60 Nlocal: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10947 ave 10947 max 10947 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: 533004 ave 533004 max 533004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533004 Ave neighs/atom = 223.576 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 : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.951 | 6.951 | 6.951 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -7781.6304 0 -7781.6304 -8734.1243 29258.229 48 0 -7782.0143 0 -7782.0143 -2096.3976 29108.546 Loop time of 0.062484 on 1 procs for 4 steps with 2384 atoms 96.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7781.6303625 -7782.01406224 -7782.01426272 Force two-norm initial, final = 210.107 0.429633 Force max component initial, final = 150.54 0.155422 Final line search alpha, max atom move = 0.00035075 5.45142e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060454 | 0.060454 | 0.060454 | 0.0 | 96.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044084 | 0.00044084 | 0.00044084 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001589 | | | 2.54 Nlocal: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10944 ave 10944 max 10944 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: 533720 ave 533720 max 533720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533720 Ave neighs/atom = 223.876 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 6 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 7.089 | 7.089 | 7.089 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7782.0143 0 -7782.0143 -2096.3976 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2384 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: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11004 ave 11004 max 11004 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: 534160 ave 534160 max 534160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 534160 Ave neighs/atom = 224.06 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) = 7.089 | 7.089 | 7.089 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 -7782.0143 -7782.0143 25.769723 126.56286 8.9249235 -2096.3976 -2096.3976 -7.6988666 -6272.9622 -8.5317853 2.4519248 1089.4792 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2384 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: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11004 ave 11004 max 11004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 267080 ave 267080 max 267080 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 534160 ave 534160 max 534160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 534160 Ave neighs/atom = 224.06 Neighbor list builds = 0 Dangerous builds = 0 2384 -7782.01426271978 eV 2.45192477591971 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01