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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -59.009251 0.0000000) to (41.723293 59.009251 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2273571 5.7244284 5.0973115 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.009251 0.0000000) to (41.723293 59.009251 5.0973115) create_atoms CPU = 0.002 seconds 1080 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2273571 5.7244284 5.0973115 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.009251 0.0000000) to (41.723293 59.009251 5.0973115) create_atoms CPU = 0.002 seconds 1080 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 2120 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.220 | 5.220 | 5.220 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8951.2565 0 -8951.2565 -5358.1601 501 0 -9014.4172 0 -9014.4172 -24156.398 Loop time of 77.6356 on 1 procs for 501 steps with 2120 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 = -8951.25654914299 -9014.40846341187 -9014.41715168427 Force two-norm initial, final = 11.692575 0.27900818 Force max component initial, final = 1.7645681 0.039396542 Final line search alpha, max atom move = 1.0000000 0.039396542 Iterations, force evaluations = 501 953 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 77.28 | 77.28 | 77.28 | 0.0 | 99.54 Neigh | 0.1697 | 0.1697 | 0.1697 | 0.0 | 0.22 Comm | 0.091871 | 0.091871 | 0.091871 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09451 | | | 0.12 Nlocal: 2120.00 ave 2120 max 2120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8080.00 ave 8080 max 8080 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: 149322.0 ave 149322 max 149322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149322 Ave neighs/atom = 70.434906 Neighbor list builds = 14 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 501 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.223 | 5.223 | 5.223 Mbytes Step Temp E_pair E_mol TotEng Press Volume 501 0 -9014.4172 0 -9014.4172 -24156.398 25099.776 522 0 -9026.2511 0 -9026.2511 17962.502 24437.774 Loop time of 2.71587 on 1 procs for 21 steps with 2120 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9014.41715168425 -9026.24393482354 -9026.25112478857 Force two-norm initial, final = 1108.4670 2.4313125 Force max component initial, final = 967.74703 1.6498451 Final line search alpha, max atom move = 5.7859905e-05 9.5459878e-05 Iterations, force evaluations = 21 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7039 | 2.7039 | 2.7039 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017519 | 0.0017519 | 0.0017519 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01023 | | | 0.38 Nlocal: 2120.00 ave 2120 max 2120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8099.00 ave 8099 max 8099 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: 149280.0 ave 149280 max 149280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149280 Ave neighs/atom = 70.415094 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.363 | 5.363 | 5.363 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9026.2511 0 -9026.2511 17962.502 Loop time of 1.897e-06 on 1 procs for 0 steps with 2120 atoms 158.1% 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 | | 1.897e-06 | | |100.00 Nlocal: 2120.00 ave 2120 max 2120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8266.00 ave 8266 max 8266 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: 152218.0 ave 152218 max 152218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152218 Ave neighs/atom = 71.800943 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.363 | 5.363 | 5.363 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 -9026.2511 -9026.2511 41.468729 118.0185 4.9933363 17962.502 17962.502 -86.076828 54079.542 -105.9599 2.3257471 5154.8997 Loop time of 1.852e-06 on 1 procs for 0 steps with 2120 atoms 216.0% 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 | | 1.852e-06 | | |100.00 Nlocal: 2120.00 ave 2120 max 2120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8266.00 ave 8266 max 8266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76109.0 ave 76109 max 76109 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 152218.0 ave 152218 max 152218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152218 Ave neighs/atom = 71.800943 Neighbor list builds = 0 Dangerous builds = 0 2120 -9026.25112478857 eV 2.32574707236216 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:21