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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -63.827493 0.0000000) to (36.848734 63.827493 6.2584463) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6690360 5.7277840 6.2584463 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -63.827493 0.0000000) to (36.848734 63.827493 6.2584463) create_atoms CPU = 0.003 seconds 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6690360 5.7277840 6.2584463 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -63.827493 0.0000000) to (36.848734 63.827493 6.2584463) create_atoms CPU = 0.003 seconds 1251 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2480 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_087820130586_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.308 | 5.308 | 5.308 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8707.5515 0 -8707.5515 4611.5534 33 0 -8749.4554 0 -8749.4554 -3228.1909 Loop time of 2.50252 on 1 procs for 33 steps with 2480 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 = -8707.55152636253 -8749.44746942592 -8749.4553985052 Force two-norm initial, final = 63.663006 0.30812342 Force max component initial, final = 11.009604 0.081358410 Final line search alpha, max atom move = 1.0000000 0.081358410 Iterations, force evaluations = 33 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4898 | 2.4898 | 2.4898 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0051567 | 0.0051567 | 0.0051567 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007555 | | | 0.30 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8227.00 ave 8227 max 8227 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: 191814.0 ave 191814 max 191814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191814 Ave neighs/atom = 77.344355 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.308 | 5.308 | 5.308 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -8749.4554 0 -8749.4554 -3228.1909 29439.259 35 0 -8749.511 0 -8749.511 -733.02334 29386.923 Loop time of 0.163409 on 1 procs for 2 steps with 2480 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 = -8749.45539850522 -8749.50555365165 -8749.51103188474 Force two-norm initial, final = 76.725785 8.1002173 Force max component initial, final = 71.598383 7.8693514 Final line search alpha, max atom move = 5.0343373e-05 0.00039616969 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16167 | 0.16167 | 0.16167 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025264 | 0.00025264 | 0.00025264 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001483 | | | 0.91 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8236.00 ave 8236 max 8236 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: 191946.0 ave 191946 max 191946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191946 Ave neighs/atom = 77.397581 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.446 | 5.446 | 5.446 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8749.511 0 -8749.511 -733.02334 Loop time of 3.628e-06 on 1 procs for 0 steps with 2480 atoms 192.9% 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 | | 3.628e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8236.00 ave 8236 max 8236 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: 191954.0 ave 191954 max 191954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191954 Ave neighs/atom = 77.400806 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.446 | 5.446 | 5.446 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 -8749.511 -8749.511 36.839206 127.65499 6.2489359 -733.02334 -733.02334 428.9265 -2731.0765 103.07996 2.2905844 1056.9996 Loop time of 2.6e-06 on 1 procs for 0 steps with 2480 atoms 192.3% 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 | | 2.6e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8236.00 ave 8236 max 8236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95977.0 ave 95977 max 95977 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191954.0 ave 191954 max 191954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191954 Ave neighs/atom = 77.400806 Neighbor list builds = 0 Dangerous builds = 0 2480 -8749.51103188474 eV 2.29058443860164 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03