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 -45.879408 0.0000000) to (32.439092 45.879408 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0072392 6.2300473 5.0973115 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -45.879408 0.0000000) to (32.439092 45.879408 5.0973115) create_atoms CPU = 0.002 seconds 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0072392 6.2300473 5.0973115 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -45.879408 0.0000000) to (32.439092 45.879408 5.0973115) create_atoms CPU = 0.002 seconds 650 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 ghost atom cutoff = 6 binsize = 3, bins = 11 31 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1284 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5407.1382 0 -5407.1382 -170.64438 141 0 -5443.1122 0 -5443.1122 -12775.109 Loop time of 11.5443 on 1 procs for 141 steps with 1284 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 = -5407.13815824851 -5443.10707769161 -5443.11221667993 Force two-norm initial, final = 27.191567 0.20255336 Force max component initial, final = 7.1119799 0.033149845 Final line search alpha, max atom move = 1.0000000 0.033149845 Iterations, force evaluations = 141 260 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.484 | 11.484 | 11.484 | 0.0 | 99.48 Neigh | 0.022362 | 0.022362 | 0.022362 | 0.0 | 0.19 Comm | 0.019373 | 0.019373 | 0.019373 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01866 | | | 0.16 Nlocal: 1284.00 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5673.00 ave 5673 max 5673 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: 99088.0 ave 99088 max 99088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99088 Ave neighs/atom = 77.171340 Neighbor list builds = 3 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 ghost atom cutoff = 6 binsize = 3, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 141 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press Volume 141 0 -5443.1122 0 -5443.1122 -12775.109 15172.518 144 0 -5443.3084 0 -5443.3084 -5332.4152 15101.517 Loop time of 0.208574 on 1 procs for 3 steps with 1284 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 = -5443.11221667993 -5443.30369906873 -5443.30844607787 Force two-norm initial, final = 118.03022 0.93783738 Force max component initial, final = 83.918684 0.65375917 Final line search alpha, max atom move = 7.2306500e-05 4.7271038e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20725 | 0.20725 | 0.20725 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022799 | 0.00022799 | 0.00022799 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001097 | | | 0.53 Nlocal: 1284.00 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5690.00 ave 5690 max 5690 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: 99056.0 ave 99056 max 99056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99056 Ave neighs/atom = 77.146417 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 ghost atom cutoff = 6 binsize = 3, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.173 | 5.173 | 5.173 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5443.3084 0 -5443.3084 -5332.4152 Loop time of 2.095e-06 on 1 procs for 0 steps with 1284 atoms 143.2% 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 | | 2.095e-06 | | |100.00 Nlocal: 1284.00 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5694.00 ave 5694 max 5694 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: 99108.0 ave 99108 max 99108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99108 Ave neighs/atom = 77.186916 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 ghost atom cutoff = 6 binsize = 3, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.173 | 5.173 | 5.173 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 -5443.3084 -5443.3084 32.364482 91.758815 5.0851541 -5332.4152 -5332.4152 69.200233 -15998.942 -67.503878 2.3210848 682.34242 Loop time of 2.019e-06 on 1 procs for 0 steps with 1284 atoms 198.1% 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 | | 2.019e-06 | | |100.00 Nlocal: 1284.00 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5694.00 ave 5694 max 5694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49554.0 ave 49554 max 49554 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 99108.0 ave 99108 max 99108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99108 Ave neighs/atom = 77.186916 Neighbor list builds = 0 Dangerous builds = 0 1284 -5443.30844607787 eV 2.32108483359859 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12