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 41.63133332492248*${_u_distance} variable xmax_converted equal 41.63133332492248*1 variable ymin_converted equal -41.63532088345722*${_u_distance} variable ymin_converted equal -41.63532088345722*1 variable ymax_converted equal 41.63532088345722*${_u_distance} variable ymax_converted equal 41.63532088345722*1 variable zmin_converted equal 0.0*${_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 41.6313333249225 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 41.6313333249225 -41.6353208834572 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 41.6313333249225 -41.6353208834572 41.6353208834572 ${zmin_converted} ${zmax_converted} units box region whole block 0 41.6313333249225 -41.6353208834572 41.6353208834572 0 ${zmax_converted} units box region whole block 0 41.6313333249225 -41.6353208834572 41.6353208834572 0 3.9875585347414 units box create_box 2 whole Created orthogonal box = (0 -41.6353 0) to (41.6313 41.6353 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 41.6353208834572 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.9652 4.9652 3.98756 create_atoms 1 region upper Created 438 atoms create_atoms CPU = 0.000252962 secs group upper type 1 438 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.698137929009748 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -41.6353208834572 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 3 0 orient y -3 10 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 10 3 0 orient y -3 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.9652 4.9652 3.98756 create_atoms 2 region lower Created 438 atoms create_atoms CPU = 0.000111103 secs group lower type 2 438 atoms in group lower displace_atoms lower move -4.698137929009748 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 11 21 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 20 atoms, new total = 856 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 = 11 21 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) = 4.962 | 4.962 | 4.962 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2869.6221 0 -2869.6221 -487.45276 263 0 -2884.8075 0 -2884.8075 -10246.414 Loop time of 1.25072 on 1 procs for 263 steps with 856 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2869.6220857 -2884.80752613 -2884.80752613 Force two-norm initial, final = 18.0935 1.87401e-05 Force max component initial, final = 4.72644 2.53632e-06 Final line search alpha, max atom move = 1 2.53632e-06 Iterations, force evaluations = 263 513 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2177 | 1.2177 | 1.2177 | 0.0 | 97.36 Neigh | 0.0062983 | 0.0062983 | 0.0062983 | 0.0 | 0.50 Comm | 0.017019 | 0.017019 | 0.017019 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009675 | | | 0.77 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6217 ave 6217 max 6217 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: 116548 ave 116548 max 116548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116548 Ave neighs/atom = 136.154 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) = 4.962 | 4.962 | 4.962 Mbytes Step Temp E_pair E_mol TotEng Press Volume 263 0 -2884.8075 0 -2884.8075 -10246.414 13823.541 1263 0 -2885.251 0 -2885.251 -1020.6198 13681.545 Loop time of 5.08376 on 1 procs for 1000 steps with 856 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2884.80752613 -2885.25102006 -2885.25102028 Force two-norm initial, final = 119.979 0.0405014 Force max component initial, final = 88.4818 0.0234273 Final line search alpha, max atom move = 0.023227 0.000544148 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8035 | 4.8035 | 4.8035 | 0.0 | 94.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.062979 | 0.062979 | 0.062979 | 0.0 | 1.24 Output | 3.6001e-05 | 3.6001e-05 | 3.6001e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2172 | | | 4.27 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6224 ave 6224 max 6224 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: 116576 ave 116576 max 116576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116576 Ave neighs/atom = 136.187 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 = 11 21 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) = 5.1 | 5.1 | 5.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2885.251 0 -2885.251 -1020.6198 Loop time of 1.19209e-06 on 1 procs for 0 steps with 856 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 | | 1.192e-06 | | |100.00 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6236 ave 6236 max 6236 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: 117048 ave 117048 max 117048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117048 Ave neighs/atom = 136.738 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) = 5.1 | 5.1 | 5.1 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 -2885.251 -2885.251 41.338674 83.270642 3.9745384 -1020.6198 -1020.6198 1.4129218 -3066.0068 2.7345001 2.5509711 641.21517 Loop time of 1.19209e-06 on 1 procs for 0 steps with 856 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 | | 1.192e-06 | | |100.00 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6236 ave 6236 max 6236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58524 ave 58524 max 58524 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117048 ave 117048 max 117048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117048 Ave neighs/atom = 136.738 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_033.3985/numatoms.out 856 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2885.25102027712-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2885.25102027712-856*${isolated_atom_energy} variable adjusted_pe_metal equal -2885.25102027712-856*-1.81000000000002 print "${adjusted_pe_metal} eV" file output/dump_033.3985/energy.out -1335.8910202771 eV print "${mindist_metal} Angstroms" file output/dump_033.3985/mindistance.out 2.55097110308602 Angstroms write_dump all cfg output/dump_033.3985/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_033.3985/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06