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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -69.720000 0.0000000) to (42.694606 69.720000 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9374714 4.9800000 5.7504086 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -69.720000 0.0000000) to (42.694606 69.720000 8.6256130) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9374714 4.9800000 5.7504086 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -69.720000 0.0000000) to (42.694606 69.720000 8.6256130) create_atoms CPU = 0.003 seconds 2358 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 43 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 6 atoms, new total = 4704 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_115454747503_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 43 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) = 10.57 | 10.57 | 10.57 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20154.127 0 -20154.127 40364.838 67 0 -20860.069 0 -20860.069 9320.2823 Loop time of 27.7326 on 1 procs for 67 steps with 4704 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 = -20154.126924203 -20860.0479518419 -20860.0687877841 Force two-norm initial, final = 615.22331 0.61461678 Force max component initial, final = 104.96014 0.059306363 Final line search alpha, max atom move = 1.0000000 0.059306363 Iterations, force evaluations = 67 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.681 | 27.681 | 27.681 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.02077 | 0.02077 | 0.02077 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03076 | | | 0.11 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12081.0 ave 12081 max 12081 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: 408780.0 ave 408780 max 408780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 408780 Ave neighs/atom = 86.900510 Neighbor list builds = 0 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 43 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.57 | 10.57 | 10.57 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -20860.069 0 -20860.069 9320.2823 51351.171 74 0 -20861.7 0 -20861.7 -154.7682 51609.654 Loop time of 1.98698 on 1 procs for 7 steps with 4704 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20860.0687877841 -20861.6979431347 -20861.6995632154 Force two-norm initial, final = 613.41115 10.957011 Force max component initial, final = 562.76820 10.117829 Final line search alpha, max atom move = 7.1513147e-05 0.00072355782 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.979 | 1.979 | 1.979 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00098158 | 0.00098158 | 0.00098158 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007048 | | | 0.35 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12051.0 ave 12051 max 12051 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: 408804.0 ave 408804 max 408804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 408804 Ave neighs/atom = 86.905612 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 44 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) = 10.09 | 10.09 | 10.09 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20861.7 0 -20861.7 -154.7682 Loop time of 2.075e-06 on 1 procs for 0 steps with 4704 atoms 192.8% 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 | | 2.075e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12071.0 ave 12071 max 12071 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: 408204.0 ave 408204 max 408204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 408204 Ave neighs/atom = 86.778061 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 44 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) = 10.09 | 10.09 | 10.09 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 -20861.7 -20861.7 42.679934 140.29608 8.619095 -154.7682 -154.7682 -313.99122 -26.006114 -124.30727 2.1975353 1708.3501 Loop time of 2.663e-06 on 1 procs for 0 steps with 4704 atoms 300.4% 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 | | 2.663e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12071.0 ave 12071 max 12071 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 204102.0 ave 204102 max 204102 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 408204.0 ave 408204 max 408204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 408204 Ave neighs/atom = 86.778061 Neighbor list builds = 0 Dangerous builds = 0 4704 -20861.6995632155 eV 2.19753527751354 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:31