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 4.050004702806472*${_u_distance} variable lattice_constant_converted equal 4.050004702806472*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 52.65006113648414*${_u_distance} variable xmax_converted equal 52.65006113648414*1 variable ymin_converted equal -52.654111141186945*${_u_distance} variable ymin_converted equal -52.654111141186945*1 variable ymax_converted equal 52.654111141186945*${_u_distance} variable ymax_converted equal 52.654111141186945*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050004702806472*${_u_distance} variable zmax_converted equal 4.050004702806472*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000470280647 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 52.6500611364841 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6500611364841 -52.6541111411869 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6500611364841 -52.6541111411869 52.6541111411869 ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6500611364841 -52.6541111411869 52.6541111411869 0 ${zmax_converted} units box region whole block 0 52.6500611364841 -52.6541111411869 52.6541111411869 0 4.05000470280647 units box create_box 2 whole Created orthogonal box = (0 -52.6541 0) to (52.6501 52.6541 4.05) 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 52.6541111411869 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -5 0 orient y 5 12 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 12 -5 0 orient y 5 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.29616 5.29616 4.05 create_atoms 1 region upper Created 678 atoms create_atoms CPU = 0.000333071 secs group upper type 1 678 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.85 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -52.6541111411869 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 5 0 orient y -5 12 0 orient z 0 0 1 lattice fcc 4.05000470280647 orient x 12 5 0 orient y -5 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.29616 5.29616 4.05 create_atoms 2 region lower Created 678 atoms create_atoms CPU = 0.000173092 secs group lower type 2 678 atoms in group lower displace_atoms lower move -5.85 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MishinFarkasMehl_1999_Al__MO_651801486679_005 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*4.05000470280647 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500235140324 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 = 13 26 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1332 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.088 | 5.088 | 5.088 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4443.1475 0 -4443.1475 -1943.4995 263 0 -4459.4992 0 -4459.4992 -6435.0869 Loop time of 2.25362 on 1 procs for 263 steps with 1332 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4443.14750731 -4459.49921871 -4459.49921871 Force two-norm initial, final = 13.9667 2.4386e-05 Force max component initial, final = 2.89146 6.35921e-06 Final line search alpha, max atom move = 1 6.35921e-06 Iterations, force evaluations = 263 517 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.201 | 2.201 | 2.201 | 0.0 | 97.66 Neigh | 0.010321 | 0.010321 | 0.010321 | 0.0 | 0.46 Comm | 0.026182 | 0.026182 | 0.026182 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01613 | | | 0.72 Nlocal: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8783 ave 8783 max 8783 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: 184940 ave 184940 max 184940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184940 Ave neighs/atom = 138.844 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) = 5.088 | 5.088 | 5.088 Mbytes Step Temp E_pair E_mol TotEng Press Volume 263 0 -4459.4992 0 -4459.4992 -6435.0869 22455.188 1263 0 -4459.8208 0 -4459.8208 -815.82083 22292.902 Loop time of 8.71652 on 1 procs for 1000 steps with 1332 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4459.49921871 -4459.82075607 -4459.82075608 Force two-norm initial, final = 124.678 0.00866329 Force max component initial, final = 91.4117 0.00687915 Final line search alpha, max atom move = 0.266809 0.00183542 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2925 | 8.2925 | 8.2925 | 0.0 | 95.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.092342 | 0.092342 | 0.092342 | 0.0 | 1.06 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3317 | | | 3.81 Nlocal: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8783 ave 8783 max 8783 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: 184976 ave 184976 max 184976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184976 Ave neighs/atom = 138.871 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 1.04222210722815e-10 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.226 | 5.226 | 5.226 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4459.8208 0 -4459.8208 -815.82083 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1332 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: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8788 ave 8788 max 8788 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: 185016 ave 185016 max 185016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185016 Ave neighs/atom = 138.901 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) = 5.226 | 5.226 | 5.226 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 -4459.8208 -4459.8208 52.485369 105.30822 4.0333516 -815.82083 -815.82083 -0.4928537 -2446.8743 -0.095348583 2.489607 1070.8248 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1332 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: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8788 ave 8788 max 8788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92508 ave 92508 max 92508 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 185016 ave 185016 max 185016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185016 Ave neighs/atom = 138.901 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_045.2397/numatoms.out 1332 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4459.82075608389-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4459.82075608389-1332*${isolated_atom_energy} variable adjusted_pe_metal equal -4459.82075608389-1332*1.04222210722815e-10 print "${adjusted_pe_metal} eV" file output/dump_045.2397/energy.out -4459.82075622271 eV print "${mindist_metal} Angstroms" file output/dump_045.2397/mindistance.out 2.48960695346347 Angstroms write_dump all cfg output/dump_045.2397/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_045.2397/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:11