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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -41.590634 0.0000000) to (29.409019 41.590634 5.1194532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2382769 5.6714501 5.1194532 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.590634 0.0000000) to (29.409019 41.590634 5.1194532) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2382769 5.6714501 5.1194532 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.590634 0.0000000) to (29.409019 41.590634 5.1194532) create_atoms CPU = 0.001 seconds 532 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1056 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_803527979660_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.021 | 5.021 | 5.021 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3627.3746 0 -3627.3746 20073.132 75 0 -3729.1502 0 -3729.1502 2323.7949 Loop time of 1.29317 on 1 procs for 75 steps with 1056 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 = -3627.37462496495 -3729.14697316301 -3729.15021805472 Force two-norm initial, final = 168.59833 0.17574234 Force max component initial, final = 31.574211 0.031736640 Final line search alpha, max atom move = 1.0000000 0.031736640 Iterations, force evaluations = 75 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.269 | 1.269 | 1.269 | 0.0 | 98.13 Neigh | 0.010271 | 0.010271 | 0.010271 | 0.0 | 0.79 Comm | 0.0073607 | 0.0073607 | 0.0073607 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006538 | | | 0.51 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6608.00 ave 6608 max 6608 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: 183376.0 ave 183376 max 183376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183376 Ave neighs/atom = 173.65152 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.021 | 5.021 | 5.021 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -3729.1502 0 -3729.1502 2323.7949 12523.614 79 0 -3729.2514 0 -3729.2514 -277.09085 12547.664 Loop time of 0.0561158 on 1 procs for 4 steps with 1056 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 = -3729.15021805472 -3729.24985244606 -3729.25141436476 Force two-norm initial, final = 51.969776 4.0891380 Force max component initial, final = 36.679228 3.1696218 Final line search alpha, max atom move = 0.00019160629 0.00060731948 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.05451 | 0.05451 | 0.05451 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003008 | 0.0003008 | 0.0003008 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001305 | | | 2.33 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6600.00 ave 6600 max 6600 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: 182544.0 ave 182544 max 182544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182544 Ave neighs/atom = 172.86364 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.159 | 5.159 | 5.159 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3729.2514 0 -3729.2514 -277.09085 Loop time of 1.924e-06 on 1 procs for 0 steps with 1056 atoms 104.0% 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 | | 1.924e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6600.00 ave 6600 max 6600 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: 182360.0 ave 182360 max 182360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182360 Ave neighs/atom = 172.68939 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.159 | 5.159 | 5.159 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 -3729.2514 -3729.2514 29.470262 83.389258 5.1058582 -277.09085 -277.09085 -306.13536 -121.49169 -403.6455 2.3905302 657.40217 Loop time of 2.34e-06 on 1 procs for 0 steps with 1056 atoms 170.9% 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 | | 2.34e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6600.00 ave 6600 max 6600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91180.0 ave 91180 max 91180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 182360.0 ave 182360 max 182360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182360 Ave neighs/atom = 172.68939 Neighbor list builds = 0 Dangerous builds = 0 1056 -3729.25141436476 eV 2.39053020094989 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01