LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -77.382770 0.0000000) to (44.674628 77.382770 7.0055406) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5913385 5.9196839 7.0055406 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.382770 0.0000000) to (44.674628 77.382770 7.0055406) create_atoms CPU = 0.008 seconds 1465 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5913385 5.9196839 7.0055406 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.382770 0.0000000) to (44.674628 77.382770 7.0055406) create_atoms CPU = 0.008 seconds 1465 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 48 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2906 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_099716416216_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.657 | 5.657 | 5.657 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9711.864 0 -9711.864 1060.016 55 0 -9739.799 0 -9739.799 -2592.4222 Loop time of 20.1028 on 1 procs for 55 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 = -9711.86403169383 -9739.78956298358 -9739.79895630352 Force two-norm initial, final = 31.294294 0.32347429 Force max component initial, final = 6.1485911 0.051734511 Final line search alpha, max atom move = 1.0000000 0.051734511 Iterations, force evaluations = 55 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.998 | 19.998 | 19.998 | 0.0 | 99.48 Neigh | 0.060548 | 0.060548 | 0.060548 | 0.0 | 0.30 Comm | 0.017356 | 0.017356 | 0.017356 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02712 | | | 0.13 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7931.00 ave 7931 max 7931 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 222982.0 ave 222982 max 222982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 222982 Ave neighs/atom = 76.731590 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.657 | 5.657 | 5.657 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -9739.799 0 -9739.799 -2592.4222 48436.959 57 0 -9739.8839 0 -9739.8839 -619.50194 48314.848 Loop time of 0.838251 on 1 procs for 2 steps with 2906 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9739.79895630355 -9739.87955726726 -9739.8839382527 Force two-norm initial, final = 95.059177 1.4869767 Force max component initial, final = 68.813876 1.0812391 Final line search alpha, max atom move = 6.0098647e-05 6.4981006e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83478 | 0.83478 | 0.83478 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068578 | 0.00068578 | 0.00068578 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002786 | | | 0.33 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7986.00 ave 7986 max 7986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 222966.0 ave 222966 max 222966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 222966 Ave neighs/atom = 76.726084 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9739.8839 0 -9739.8839 -619.50194 Loop time of 6.184e-06 on 1 procs for 0 steps with 2906 atoms 194.0% 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 | | 6.184e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8002.00 ave 8002 max 8002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223082.0 ave 223082 max 223082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223082 Ave neighs/atom = 76.766001 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 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 -9739.8839 -9739.8839 44.616017 154.76554 6.9970593 -619.50194 -619.50194 -31.998958 -1862.3186 35.811736 2.566618 1548.961 Loop time of 6.485e-06 on 1 procs for 0 steps with 2906 atoms 339.2% 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 | | 6.485e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8002.00 ave 8002 max 8002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111541.0 ave 111541 max 111541 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223082.0 ave 223082 max 223082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223082 Ave neighs/atom = 76.766001 Neighbor list builds = 0 Dangerous builds = 0 2906 -9739.8839382527 eV 2.56661803107866 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22