LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 3.987558534741402*${_u_distance} variable lattice_constant_converted equal 3.987558534741402*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 70.9964612678161*${_u_distance} variable xmax_converted equal 70.9964612678161*1 variable ymin_converted equal -71.00044882635085*${_u_distance} variable ymin_converted equal -71.00044882635085*1 variable ymax_converted equal 71.00044882635085*${_u_distance} variable ymax_converted equal 71.00044882635085*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.987558534741402*${_u_distance} variable zmax_converted equal 3.987558534741402*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.9875585347414 Lattice spacing in x,y,z = 3.98756 3.98756 3.98756 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 70.9964612678161 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 70.9964612678161 -71.0004488263508 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 70.9964612678161 -71.0004488263508 71.0004488263508 ${zmin_converted} ${zmax_converted} units box region whole block 0 70.9964612678161 -71.0004488263508 71.0004488263508 0 ${zmax_converted} units box region whole block 0 70.9964612678161 -71.0004488263508 71.0004488263508 0 3.9875585347414 units box create_box 2 whole Created orthogonal box = (0 -71.0004 0) to (70.9965 71.0004 3.98756) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 71.0004488263508 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -11 0 orient y 11 14 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 14 -11 0 orient y 11 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.59909 5.59909 3.98756 create_atoms 1 region upper Created 1270 atoms create_atoms CPU = 0.000351906 secs group upper type 1 1270 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.012022216644183 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -71.0004488263508 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 11 0 orient y -11 14 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 14 11 0 orient y -11 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.59909 5.59909 3.98756 create_atoms 2 region lower Created 1270 atoms create_atoms CPU = 0.000225067 secs group lower type 2 1270 atoms in group lower displace_atoms lower move -8.012022216644183 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000 pair_coeff * * Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*3.9875585347414 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.9937792673707 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 ghost atom cutoff = 8 binsize = 4, bins = 18 36 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: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2514 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/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 ghost atom cutoff = 8 binsize = 4, bins = 18 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.03 | 10.03 | 10.03 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8463.2325 0 -8463.2325 1155.9741 286 0 -8501.1403 0 -8501.1403 -6020.7743 Loop time of 3.98595 on 1 procs for 286 steps with 2514 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8463.23250135 -8501.14031179 -8501.14031179 Force two-norm initial, final = 31.2464 4.55835e-05 Force max component initial, final = 5.14515 7.66334e-06 Final line search alpha, max atom move = 1 7.66334e-06 Iterations, force evaluations = 286 551 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8996 | 3.8996 | 3.8996 | 0.0 | 97.83 Neigh | 0.013135 | 0.013135 | 0.013135 | 0.0 | 0.33 Comm | 0.044147 | 0.044147 | 0.044147 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02905 | | | 0.73 Nlocal: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14616 ave 14616 max 14616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 347548 ave 347548 max 347548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 347548 Ave neighs/atom = 138.245 Neighbor list builds = 2 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 (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 10.03 | 10.03 | 10.03 Mbytes Step Temp E_pair E_mol TotEng Press Volume 286 0 -8501.1403 0 -8501.1403 -6020.7743 40200.816 1286 0 -8501.4257 0 -8501.4257 -1656.427 40010.567 Loop time of 14.0201 on 1 procs for 1000 steps with 2514 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -8501.14031179 -8501.42565037 -8501.42565042 Force two-norm initial, final = 168.244 0.0268641 Force max component initial, final = 121.472 0.0210844 Final line search alpha, max atom move = 0.19994 0.00421562 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.355 | 13.355 | 13.355 | 0.0 | 95.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1456 | 0.1456 | 0.1456 | 0.0 | 1.04 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5196 | | | 3.71 Nlocal: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14601 ave 14601 max 14601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346340 ave 346340 max 346340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346340 Ave neighs/atom = 137.765 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal -1.81000000000002 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/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 ghost atom cutoff = 8 binsize = 4, bins = 18 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 9.539 | 9.539 | 9.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8501.4257 0 -8501.4257 -1656.427 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2514 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14606 ave 14606 max 14606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346612 ave 346612 max 346612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346612 Ave neighs/atom = 137.873 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom 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 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 9.539 | 9.539 | 9.539 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 -8501.4257 -8501.4257 70.911625 142.0009 3.9734356 -1656.427 -1656.427 -0.36113196 -4968.0787 -0.84131132 2.5456628 555.16192 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2514 atoms 0.0% 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 | | 1.907e-06 | | |100.00 Nlocal: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14606 ave 14606 max 14606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173306 ave 173306 max 173306 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346612 ave 346612 max 346612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346612 Ave neighs/atom = 137.873 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_076.3145/numatoms.out 2514 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8501.42565042024-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8501.42565042024-2514*${isolated_atom_energy} variable adjusted_pe_metal equal -8501.42565042024-2514*-1.81000000000002 print "${adjusted_pe_metal} eV" file output/dump_076.3145/energy.out -3951.08565042019 eV print "${mindist_metal} Angstroms" file output/dump_076.3145/mindistance.out 2.54566283044201 Angstroms write_dump all cfg output/dump_076.3145/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_076.3145/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:18