LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 4.04969653487 Lattice spacing in x,y,z = 4.0497 4.0497 4.0497 region whole block 0 83.09282575728504 -83.0968754538199 83.0968754538199 0 4.04969653487 units box create_box 2 whole Created orthogonal box = (0 -83.0969 0) to (83.0928 83.0969 4.0497) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 83.0968754538199 INF INF units box lattice fcc 4.04969653487 orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72373 5.72373 4.0497 create_atoms 1 region upper Created 1686 atoms group upper type 1 1686 atoms in group upper mass 1 26.981538 displace_atoms upper move 9.233228037907434 0 0.3333333333333333 region lower block INF INF -83.0968754538199 0.0 INF INF units box lattice fcc 4.04969653487 orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72373 5.72373 4.0497 create_atoms 2 region lower Created 1686 atoms group lower type 2 1686 atoms in group lower displace_atoms lower move -9.233228037907434 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial EAM_Dynamo_Vailhe_Farkas_CoAl__MO_284963179498_004 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 2.02484826743 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 22 44 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: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Deleted 38 atoms, new total = 3334 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 22 44 2 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) = 10.05 | 10.05 | 10.05 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11184.751 0 -11184.751 -462.9372 400 0 -11221.393 0 -11221.393 -6773.301 Loop time of 4.40982 on 1 procs for 400 steps with 3334 atoms 100.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11184.7509107 -11221.3928799 -11221.3928799 Force two-norm initial, final = 37.3755 4.09782e-05 Force max component initial, final = 7.14797 7.36519e-06 Final line search alpha, max atom move = 1 7.36519e-06 Iterations, force evaluations = 400 788 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2901 | 4.2901 | 4.2901 | 0.0 | 97.29 Neigh | 0.030947 | 0.030947 | 0.030947 | 0.0 | 0.70 Comm | 0.042408 | 0.042408 | 0.042408 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04635 | | | 1.05 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18231 ave 18231 max 18231 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 318129 ave 318129 max 318129 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318129 Ave neighs/atom = 95.4196 Neighbor list builds = 4 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) = 10.05 | 10.05 | 10.05 Mbytes Step Temp E_pair E_mol TotEng Press Volume 400 0 -11221.393 0 -11221.393 -6773.301 55924.318 1087 0 -11222.034 0 -11222.034 -1739.0441 55572.541 Loop time of 7.97969 on 1 procs for 687 steps with 3334 atoms 100.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -11221.3928799 -11222.0338453 -11222.0338453 Force two-norm initial, final = 276.287 0.00330851 Force max component initial, final = 210.224 0.00288686 Final line search alpha, max atom move = 0.0103625 2.99152e-05 Iterations, force evaluations = 687 1384 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6063 | 7.6063 | 7.6063 | 0.0 | 95.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.067295 | 0.067295 | 0.067295 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3061 | | | 3.84 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18241 ave 18241 max 18241 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 318947 ave 318947 max 318947 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318947 Ave neighs/atom = 95.665 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 22 44 2 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) = 9.565 | 9.565 | 9.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11222.034 0 -11222.034 -1739.0441 Loop time of 0 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18256 ave 18256 max 18256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 337752 ave 337752 max 337752 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 = 337752 Ave neighs/atom = 101.305 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) = 9.565 | 9.565 | 9.565 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -11222.034 82.942204 166.19375 4.0315309 -1739.0441 0.0022605102 -5217.0518 -0.082856005 -11222.034 2.6236869 343.89314 Loop time of 0 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18256 ave 18256 max 18256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 337752 ave 337752 max 337752 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 401064 ave 401064 max 401064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401064 Ave neighs/atom = 120.295 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_086.0501/energy.out -11222.0338452583 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_086.0501/numatoms.out 3334 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_086.0501/mindistance.out 2.62368694715514 write_dump all cfg output/dump_086.0501/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_086.0501/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:12