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 = 4.1288715 4.1288715 4.1288715 Created orthogonal box = (0.0000000 -62.344592 0.0000000) to (44.084284 62.344592 5.8391060) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9606764 7.1094710 5.8391060 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -62.344592 0.0000000) to (44.084284 62.344592 5.8391060) create_atoms CPU = 0.008 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9606764 7.1094710 5.8391060 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -62.344592 0.0000000) to (44.084284 62.344592 5.8391060) create_atoms CPU = 0.007 seconds 916 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 10 28 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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_122703700223_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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.985 | 5.985 | 5.985 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6381.8804 0 -6381.8804 18700.873 45 0 -6765.6106 0 -6765.6106 1395.0292 Loop time of 3.87699 on 1 procs for 45 steps with 1824 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 = -6381.88041484769 -6765.60395295064 -6765.61061228086 Force two-norm initial, final = 405.55795 0.18949669 Force max component initial, final = 95.135754 0.022511656 Final line search alpha, max atom move = 1.0000000 0.022511656 Iterations, force evaluations = 45 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7501 | 3.7501 | 3.7501 | 0.0 | 96.73 Neigh | 0.092638 | 0.092638 | 0.092638 | 0.0 | 2.39 Comm | 0.017937 | 0.017937 | 0.017937 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01631 | | | 0.42 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10774.0 ave 10774 max 10774 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: 328888.0 ave 328888 max 328888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328888 Ave neighs/atom = 180.31140 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.988 | 5.988 | 5.988 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -6765.6106 0 -6765.6106 1395.0292 32096.593 49 0 -6765.6943 0 -6765.6943 45.392993 32138.482 Loop time of 0.329016 on 1 procs for 4 steps with 1824 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 = -6765.61061228085 -6765.69383411533 -6765.69428608524 Force two-norm initial, final = 62.139567 3.0416595 Force max component initial, final = 59.709325 3.0255965 Final line search alpha, max atom move = 0.00021589785 0.00065321978 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32311 | 0.32311 | 0.32311 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013639 | 0.0013639 | 0.0013639 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004544 | | | 1.38 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10774.0 ave 10774 max 10774 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: 326480.0 ave 326480 max 326480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 326480 Ave neighs/atom = 178.99123 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 6.126 | 6.126 | 6.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6765.6943 0 -6765.6943 45.392993 Loop time of 6.585e-06 on 1 procs for 0 steps with 1824 atoms 182.2% 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 | | 6.585e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10774.0 ave 10774 max 10774 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: 324672.0 ave 324672 max 324672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324672 Ave neighs/atom = 178.00000 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 6.126 | 6.126 | 6.126 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 -6765.6943 -6765.6943 44.042457 125.06215 5.8348264 45.392993 45.392993 -6.7323919 151.28404 -8.3726656 2.7401325 842.03752 Loop time of 7.518e-06 on 1 procs for 0 steps with 1824 atoms 252.7% 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 | | 7.518e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10774.0 ave 10774 max 10774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162336.0 ave 162336 max 162336 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 324672.0 ave 324672 max 324672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324672 Ave neighs/atom = 178.00000 Neighbor list builds = 0 Dangerous builds = 0 1824 -6765.69428608524 eV 2.74013253266339 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06