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 -54.581224 0.0000000) to (38.594754 54.581224 5.1120000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0939085 5.2666093 5.1120000 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.581224 0.0000000) to (38.594754 54.581224 5.1120000) create_atoms CPU = 0.006 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0939085 5.2666093 5.1120000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.581224 0.0000000) to (38.594754 54.581224 5.1120000) create_atoms CPU = 0.005 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 15 40 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 16 atoms, new total = 1812 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 = 15 40 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) = 4.754 | 4.754 | 4.754 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6211.2001 0 -6211.2001 20963.213 18 0 -6403.0066 0 -6403.0066 -719.98056 Loop time of 0.863841 on 1 procs for 18 steps with 1812 atoms 60.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6211.20008843873 -6403.00224753989 -6403.00657266279 Force two-norm initial, final = 299.61231 1.2889029 Force max component initial, final = 70.415438 0.093667714 Final line search alpha, max atom move = 0.0026006274 0.00024359482 Iterations, force evaluations = 18 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84822 | 0.84822 | 0.84822 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0074877 | 0.0074877 | 0.0074877 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008134 | | | 0.94 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5844.00 ave 5844 max 5844 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: 97512.0 ave 97512 max 97512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97512 Ave neighs/atom = 53.814570 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 = 15 40 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.137 | 5.137 | 5.137 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -6403.0066 0 -6403.0066 -719.98056 21537.356 19 0 -6403.008 0 -6403.008 -669.74787 21536.563 Loop time of 0.16869 on 1 procs for 1 steps with 1812 atoms 65.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6403.00657266278 -6403.00657266278 -6403.00795607011 Force two-norm initial, final = 33.268129 32.291097 Force max component initial, final = 24.630310 23.714178 Final line search alpha, max atom move = 1.2687619e-06 3.0087646e-05 Iterations, force evaluations = 1 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16146 | 0.16146 | 0.16146 | 0.0 | 95.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013482 | 0.0013482 | 0.0013482 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005882 | | | 3.49 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6022.00 ave 6022 max 6022 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: 98248.0 ave 98248 max 98248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98248 Ave neighs/atom = 54.220751 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 = 15 40 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) = 5.275 | 5.275 | 5.275 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 6406.4208 0 6406.4208 -669.74787 Loop time of 7.006e-06 on 1 procs for 0 steps with 1812 atoms 128.5% 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 | | 7.006e-06 | | |100.00 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6022.00 ave 6022 max 6022 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: 98248.0 ave 98248 max 98248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98248 Ave neighs/atom = 54.220751 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 = 15 40 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) = 5.275 | 5.275 | 5.275 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 6406.4208 -6403.008 38.59388 109.16431 5.1118403 -669.74787 -669.74787 -1266.9325 1021.8103 -1764.1214 2.3590704 686.6774 Loop time of 8.71e-06 on 1 procs for 0 steps with 1812 atoms 160.7% 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 | | 8.71e-06 | | |100.00 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6022.00 ave 6022 max 6022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49124.0 ave 49124 max 49124 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98248.0 ave 98248 max 98248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98248 Ave neighs/atom = 54.220751 Neighbor list builds = 0 Dangerous builds = 0 1812 6406.42082820696 eV 2.35907044004855 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01