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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -38.425106 0.0000000) to (38.425106 38.425106 3.6147299) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1006777 5.1006777 3.6147299 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -38.425106 0.0000000) to (38.425106 38.425106 3.6147299) create_atoms CPU = 0.002 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1006777 5.1006777 3.6147299 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.425106 0.0000000) to (38.425106 38.425106 3.6147299) create_atoms CPU = 0.001 seconds 454 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 894 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_887933271505_002#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.550 | 4.550 | 4.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3030.3225 0 -3030.3225 26264.893 35 0 -3152.0138 0 -3152.0138 -1316.1029 Loop time of 1.21886 on 1 procs for 35 steps with 894 atoms 34.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3030.32252694459 -3152.01371744218 -3152.01377121042 Force two-norm initial, final = 244.92267 0.16616568 Force max component initial, final = 80.654163 0.026828586 Final line search alpha, max atom move = 0.0019531250 5.2399581e-05 Iterations, force evaluations = 35 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2054 | 1.2054 | 1.2054 | 0.0 | 98.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0069143 | 0.0069143 | 0.0069143 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00653 | | | 0.54 Nlocal: 894.000 ave 894 max 894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5012.00 ave 5012 max 5012 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: 48016.0 ave 48016 max 48016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48016 Ave neighs/atom = 53.709172 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.550 | 4.550 | 4.550 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -3152.0138 0 -3152.0138 -1316.1029 10674.216 41 0 -3152.502 0 -3152.502 -240.14446 10665.259 Loop time of 0.122046 on 1 procs for 6 steps with 894 atoms 40.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3152.01377121043 -3152.50121031067 -3152.50195727511 Force two-norm initial, final = 35.273608 3.6512364 Force max component initial, final = 22.478298 2.5580134 Final line search alpha, max atom move = 0.00022142482 0.00056640768 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11807 | 0.11807 | 0.11807 | 0.0 | 96.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061465 | 0.00061465 | 0.00061465 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003361 | | | 2.75 Nlocal: 894.000 ave 894 max 894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4997.00 ave 4997 max 4997 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: 48380.0 ave 48380 max 48380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48380 Ave neighs/atom = 54.116331 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.688 | 4.688 | 4.688 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 3156.4801 0 3156.4801 -240.14446 Loop time of 3.648e-06 on 1 procs for 0 steps with 894 atoms 109.6% 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 | | 3.648e-06 | | |100.00 Nlocal: 894.000 ave 894 max 894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5006.00 ave 5006 max 5006 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: 48448.0 ave 48448 max 48448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48448 Ave neighs/atom = 54.192394 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 14 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.688 | 4.688 | 4.688 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 3156.4801 -3152.502 38.315714 76.614964 3.6331297 -240.14446 -240.14446 -380.7017 -383.09836 43.366676 2.2509316 198.8263 Loop time of 3.908e-06 on 1 procs for 0 steps with 894 atoms 204.7% 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 | | 3.908e-06 | | |100.00 Nlocal: 894.000 ave 894 max 894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5006.00 ave 5006 max 5006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24224.0 ave 24224 max 24224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48448.0 ave 48448 max 48448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48448 Ave neighs/atom = 54.192394 Neighbor list builds = 0 Dangerous builds = 0 894 3156.48008224561 eV 2.25093163042253 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01