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 = 2.8553128 2.8553128 2.8553128 Created orthogonal box = (0.0000000 -40.782024 0.0000000) to (28.837246 40.782024 4.0380221) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5234895 3.5984139 4.0380221 Created 407 atoms using lattice units in orthogonal box = (0.0000000 -40.782024 0.0000000) to (28.837246 40.782024 4.0380221) create_atoms CPU = 0.003 seconds 407 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5234895 3.5984139 4.0380221 Created 409 atoms using lattice units in orthogonal box = (0.0000000 -40.782024 0.0000000) to (28.837246 40.782024 4.0380221) create_atoms CPU = 0.003 seconds 409 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 23 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 811 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_884343146310_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.944 | 4.944 | 4.944 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2198.3586 0 -2198.3586 247715.66 85 0 -3237.1919 0 -3237.1919 -2314.6969 Loop time of 2.01036 on 1 procs for 85 steps with 811 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 = -2198.35858491864 -3237.18889820419 -3237.19189749524 Force two-norm initial, final = 2798.2159 0.18303347 Force max component initial, final = 917.34821 0.054482378 Final line search alpha, max atom move = 1.0000000 0.054482378 Iterations, force evaluations = 85 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9394 | 1.9394 | 1.9394 | 0.0 | 96.47 Neigh | 0.033503 | 0.033503 | 0.033503 | 0.0 | 1.67 Comm | 0.019771 | 0.019771 | 0.019771 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0177 | | | 0.88 Nlocal: 811.000 ave 811 max 811 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5651.00 ave 5651 max 5651 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: 110594.0 ave 110594 max 110594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110594 Ave neighs/atom = 136.36745 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.946 | 4.946 | 4.946 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -3237.1919 0 -3237.1919 -2314.6969 9497.7609 87 0 -3237.202 0 -3237.202 -2.8637058 9485.0869 Loop time of 0.0684963 on 1 procs for 2 steps with 811 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 = -3237.19189749522 -3237.20174808934 -3237.20203964951 Force two-norm initial, final = 24.311098 0.19663693 Force max component initial, final = 17.269876 0.064284611 Final line search alpha, max atom move = 0.00044933317 2.8885208e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065966 | 0.065966 | 0.065966 | 0.0 | 96.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060558 | 0.00060558 | 0.00060558 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001925 | | | 2.81 Nlocal: 811.000 ave 811 max 811 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5634.00 ave 5634 max 5634 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: 110412.0 ave 110412 max 110412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110412 Ave neighs/atom = 136.14303 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.084 | 5.084 | 5.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3237.202 0 -3237.202 -2.8637058 Loop time of 6.245e-06 on 1 procs for 0 steps with 811 atoms 208.2% 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 | | 6.245e-06 | | |100.00 Nlocal: 811.000 ave 811 max 811 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5634.00 ave 5634 max 5634 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: 110430.0 ave 110430 max 110430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110430 Ave neighs/atom = 136.16523 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.084 | 5.084 | 5.084 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 -3237.202 -3237.202 28.832348 81.526343 4.0351839 -2.8637058 -2.8637058 -0.79188549 -10.853636 3.0544041 2.2308368 407.77502 Loop time of 6.876e-06 on 1 procs for 0 steps with 811 atoms 261.8% 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 | | 6.876e-06 | | |100.00 Nlocal: 811.000 ave 811 max 811 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5634.00 ave 5634 max 5634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55215.0 ave 55215 max 55215 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110430.0 ave 110430 max 110430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110430 Ave neighs/atom = 136.16523 Neighbor list builds = 0 Dangerous builds = 0 811 -3237.20203964951 eV 2.23083682422068 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02