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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -67.048265 0.0000000) to (23.705141 67.048265 5.1123823) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0641059 6.2370479 5.1123823 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -67.048265 0.0000000) to (23.705141 67.048265 5.1123823) create_atoms CPU = 0.002 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0641059 6.2370479 5.1123823 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -67.048265 0.0000000) to (23.705141 67.048265 5.1123823) create_atoms CPU = 0.002 seconds 690 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1376 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.522 | 5.522 | 5.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4795.776 0 -4795.776 9050.2739 90 0 -4864.3074 0 -4864.3074 1653.1797 Loop time of 1.71276 on 1 procs for 90 steps with 1376 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4795.77599131128 -4864.30301070786 -4864.30736249079 Force two-norm initial, final = 53.365772 0.19103696 Force max component initial, final = 10.648058 0.032557775 Final line search alpha, max atom move = 1.0000000 0.032557775 Iterations, force evaluations = 90 173 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6773 | 1.6773 | 1.6773 | 0.0 | 97.93 Neigh | 0.012725 | 0.012725 | 0.012725 | 0.0 | 0.74 Comm | 0.012323 | 0.012323 | 0.012323 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01041 | | | 0.61 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8752.00 ave 8752 max 8752 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: 227216.0 ave 227216 max 227216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227216 Ave neighs/atom = 165.12791 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.522 | 5.522 | 5.522 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -4864.3074 0 -4864.3074 1653.1797 16251.124 93 0 -4864.3739 0 -4864.3739 137.71339 16268.667 Loop time of 0.0491977 on 1 procs for 3 steps with 1376 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4864.30736249079 -4864.37284549973 -4864.37388955414 Force two-norm initial, final = 50.903769 2.5457479 Force max component initial, final = 44.428441 2.0115183 Final line search alpha, max atom move = 0.00020152799 0.00040537725 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.047518 | 0.047518 | 0.047518 | 0.0 | 96.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032437 | 0.00032437 | 0.00032437 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001356 | | | 2.76 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8728.00 ave 8728 max 8728 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: 231408.0 ave 231408 max 231408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231408 Ave neighs/atom = 168.17442 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.660 | 5.660 | 5.660 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4864.3739 0 -4864.3739 137.71339 Loop time of 1.534e-06 on 1 procs for 0 steps with 1376 atoms 195.6% 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 | | 1.534e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8728.00 ave 8728 max 8728 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: 229920.0 ave 229920 max 229920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229920 Ave neighs/atom = 167.09302 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.660 | 5.660 | 5.660 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 -4864.3739 -4864.3739 23.756447 133.88046 5.1150899 137.71339 137.71339 198.5278 99.635984 114.97638 2.3953337 614.97496 Loop time of 1.723e-06 on 1 procs for 0 steps with 1376 atoms 174.1% 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 | | 1.723e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8728.00 ave 8728 max 8728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114960.0 ave 114960 max 114960 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 229920.0 ave 229920 max 229920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229920 Ave neighs/atom = 167.09302 Neighbor list builds = 0 Dangerous builds = 0 1376 -4864.37388955414 eV 2.39533369817741 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02