LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 4.05000464022 Lattice spacing in x,y,z = 4.05 4.05 4.05 region whole block 0 21.809942457244183 -43.62393491912859 43.62393491912859 0 4.05000464022 units box create_box 2 whole Created orthogonal box = (0 -43.6239 0) to (21.8099 43.6239 4.05) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 43.62393491912859 INF INF units box lattice fcc 4.05000464022 orient x 5 -2 0 orient y 2 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.26447 5.26447 4.05 create_atoms 1 region upper Created 233 atoms group upper type 1 233 atoms in group upper mass 1 26.981538 displace_atoms upper move 2.4233241632105265 0 0.3333333333333333 region lower block INF INF -43.62393491912859 0.0 INF INF units box lattice fcc 4.05000464022 orient x 5 2 0 orient y -2 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.26447 5.26447 4.05 create_atoms 2 region lower Created 233 atoms group lower type 2 233 atoms in group lower displace_atoms lower move -2.4233241632105265 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial EAM_Dynamo_Mishin_Farkas_Al__MO_651801486679_004 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 2.02500232011 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 6 22 1 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: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Deleted 8 atoms, new total = 458 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Per MPI rank memory allocation (min/avg/max) = 4.425 | 4.425 | 4.425 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1522.726 0 -1522.726 36.466249 211 0 -1532.3069 0 -1532.3069 -4115.9149 Loop time of 0.533837 on 1 procs for 211 steps with 458 atoms 99.7% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1522.72602908 -1532.30694305 -1532.30694305 Force two-norm initial, final = 11.7771 2.73633e-06 Force max component initial, final = 3.58116 7.06125e-07 Final line search alpha, max atom move = 1 7.06125e-07 Iterations, force evaluations = 211 415 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52207 | 0.52207 | 0.52207 | 0.0 | 97.80 Neigh | 0.0011799 | 0.0011799 | 0.0011799 | 0.0 | 0.22 Comm | 0.0063219 | 0.0063219 | 0.0063219 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004265 | | | 0.80 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4332 ave 4332 max 4332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54746 ave 54746 max 54746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54746 Ave neighs/atom = 119.533 Neighbor list builds = 1 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 4.425 | 4.425 | 4.425 Mbytes Step Temp E_pair E_mol TotEng Press Volume 211 0 -1532.3069 0 -1532.3069 -4115.9149 7706.6365 1211 0 -1532.3663 0 -1532.3663 8.8074134 7665.8358 Loop time of 2.74121 on 1 procs for 1000 steps with 458 atoms 100.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1532.30694305 -1532.36633881 -1532.36633881 Force two-norm initial, final = 31.3377 0.00158551 Force max component initial, final = 23.4033 0.00124007 Final line search alpha, max atom move = 1 0.00124007 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5838 | 2.5838 | 2.5838 | 0.0 | 94.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.029423 | 0.029423 | 0.029423 | 0.0 | 1.07 Output | 1.0014e-05 | 1.0014e-05 | 1.0014e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.128 | | | 4.67 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4312 ave 4312 max 4312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54757 ave 54757 max 54757 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54757 Ave neighs/atom = 119.557 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 compute csym all centro/atom fcc compute csymsum all reduce sum c_csym compute eng all pe/atom compute eatoms all reduce sum c_eng compute distance all pair/local dist compute mindist all reduce min c_distance reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 4.563 | 4.563 | 4.563 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1532.3663 0 -1532.3663 8.8074134 Loop time of 0 on 1 procs for 0 steps with 458 atoms 0.0% CPU use with 1 MPI tasks x no 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 | | 0 | | | 0.00 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4312 ave 4312 max 4312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54777 ave 54777 max 54777 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54777 Ave neighs/atom = 119.6 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms c_mindist c_csymsum run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 4.563 | 4.563 | 4.563 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -1532.3663 21.763405 87.24787 4.0371774 8.8074134 0.25862362 25.970435 0.19318123 -1532.3663 2.4966837 436.60942 Loop time of 9.53674e-07 on 1 procs for 0 steps with 458 atoms 0.0% CPU use with 1 MPI tasks x no 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 | | 9.537e-07 | | |100.00 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4312 ave 4312 max 4312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54777 ave 54777 max 54777 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63588 ave 63588 max 63588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63588 Ave neighs/atom = 138.838 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_043.6028/energy.out -1532.36633881377 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_043.6028/numatoms.out 458 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_043.6028/mindistance.out 2.49668372047714 write_dump all cfg output/dump_043.6028/dump_post.cfg mass type xs ys zs id type xs ys zs c_csym c_eng modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_043.6028/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03