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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -44.162197 0.0000000) to (54.087425 44.162197 10.314067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8838541 6.4235923 6.8760448 Created 1317 atoms using lattice units in orthogonal box = (0.0000000 -44.162197 0.0000000) to (54.087425 44.162197 10.314067) create_atoms CPU = 0.002 seconds 1317 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8838541 6.4235923 6.8760448 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -44.162197 0.0000000) to (54.087425 44.162197 10.314067) create_atoms CPU = 0.002 seconds 1323 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 13 20 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2640 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_878712978062_003#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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 6.459 | 6.459 | 6.459 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8802.4067 0 -8802.4067 89601.657 72 0 -9824.3768 0 -9824.3768 2689.9165 Loop time of 4.06231 on 1 procs for 72 steps with 2640 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8802.40666449284 -9824.36724569253 -9824.37682807283 Force two-norm initial, final = 2478.3604 0.19178601 Force max component initial, final = 756.74055 0.057812221 Final line search alpha, max atom move = 1.0000000 0.057812221 Iterations, force evaluations = 72 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9235 | 3.9235 | 3.9235 | 0.0 | 96.58 Neigh | 0.10866 | 0.10866 | 0.10866 | 0.0 | 2.67 Comm | 0.012825 | 0.012825 | 0.012825 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0173 | | | 0.43 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8988.00 ave 8988 max 8988 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: 453482.0 ave 453482 max 453482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 453482 Ave neighs/atom = 171.77348 Neighbor list builds = 4 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.459 | 6.459 | 6.459 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -9824.3768 0 -9824.3768 2689.9165 49272.765 77 0 -9824.7147 0 -9824.7147 207.14586 49576.206 Loop time of 0.174997 on 1 procs for 5 steps with 2640 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 = -9824.37682807285 -9824.70589188326 -9824.71471160259 Force two-norm initial, final = 146.72292 13.158160 Force max component initial, final = 104.59399 10.897451 Final line search alpha, max atom move = 7.0110248e-05 0.00076402298 Iterations, force evaluations = 5 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17234 | 0.17234 | 0.17234 | 0.0 | 98.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039489 | 0.00039489 | 0.00039489 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002266 | | | 1.29 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8990.00 ave 8990 max 8990 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: 453518.0 ave 453518 max 453518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 453518 Ave neighs/atom = 171.78712 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 6.597 | 6.597 | 6.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9824.7147 0 -9824.7147 207.14586 Loop time of 1.717e-06 on 1 procs for 0 steps with 2640 atoms 174.7% 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 | | 1.717e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8988.00 ave 8988 max 8988 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: 451782.0 ave 451782 max 451782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 451782 Ave neighs/atom = 171.12955 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 6.597 | 6.597 | 6.597 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 -9824.7147 -9824.7147 54.063284 88.70703 10.337436 207.14586 207.14586 31.031014 353.7035 236.70307 2.7127584 3149.1542 Loop time of 2.606e-06 on 1 procs for 0 steps with 2640 atoms 230.2% 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 | | 2.606e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8988.00 ave 8988 max 8988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 225891.0 ave 225891 max 225891 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 451782.0 ave 451782 max 451782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 451782 Ave neighs/atom = 171.12955 Neighbor list builds = 0 Dangerous builds = 0 2640 -9824.71471160259 eV 2.71275842148508 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05