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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -36.865912 0.0000000) to (18.432956 36.865912 3.6150001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2537591 4.2537591 3.6150001 Created 207 atoms using lattice units in orthogonal box = (0.0000000 -36.865912 0.0000000) to (18.432956 36.865912 3.6150001) create_atoms CPU = 0.002 seconds 207 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2537591 4.2537591 3.6150001 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -36.865912 0.0000000) to (18.432956 36.865912 3.6150001) create_atoms CPU = 0.001 seconds 209 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 17 1 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 412 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1393.4246 0 -1393.4246 34212.561 50 0 -1451.1369 0 -1451.1369 -5148.3044 Loop time of 1.10546 on 1 procs for 50 steps with 412 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 = -1393.42464644809 -1451.13560772975 -1451.13687466548 Force two-norm initial, final = 175.01220 0.10856316 Force max component initial, final = 61.380293 0.016377777 Final line search alpha, max atom move = 1.0000000 0.016377777 Iterations, force evaluations = 50 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0737 | 1.0737 | 1.0737 | 0.0 | 97.13 Neigh | 0.012468 | 0.012468 | 0.012468 | 0.0 | 1.13 Comm | 0.011688 | 0.011688 | 0.011688 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007622 | | | 0.69 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5026.00 ave 5026 max 5026 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: 92314.0 ave 92314 max 92314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92314 Ave neighs/atom = 224.06311 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.493 | 4.493 | 4.493 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -1451.1369 0 -1451.1369 -5148.3044 4913.1302 54 0 -1451.1715 0 -1451.1715 -288.72889 4895.76 Loop time of 0.0822139 on 1 procs for 4 steps with 412 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1451.13687466548 -1451.17125336054 -1451.17152585712 Force two-norm initial, final = 27.635003 1.6624349 Force max component initial, final = 18.459131 1.2114174 Final line search alpha, max atom move = 0.00079641310 0.00096478865 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.079267 | 0.079267 | 0.079267 | 0.0 | 96.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075969 | 0.00075969 | 0.00075969 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002187 | | | 2.66 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014.00 ave 5014 max 5014 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: 92286.0 ave 92286 max 92286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92286 Ave neighs/atom = 223.99515 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1451.1715 0 -1451.1715 -288.72889 Loop time of 6.395e-06 on 1 procs for 0 steps with 412 atoms 187.6% 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 | | 6.395e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014.00 ave 5014 max 5014 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: 92408.0 ave 92408 max 92408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92408 Ave neighs/atom = 224.29126 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.631 | 4.631 | 4.631 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 -1451.1715 -1451.1715 18.406592 73.539882 3.6167943 -288.72889 -288.72889 -348.95665 -395.41395 -121.81608 2.3431384 200.57735 Loop time of 6.886e-06 on 1 procs for 0 steps with 412 atoms 261.4% 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 | | 6.886e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014.00 ave 5014 max 5014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46204.0 ave 46204 max 46204 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 92408.0 ave 92408 max 92408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92408 Ave neighs/atom = 224.29126 Neighbor list builds = 0 Dangerous builds = 0 412 -1451.17152585712 eV 2.34313836077923 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01