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 4.050000011920929*${_u_distance} variable lattice_constant_converted equal 4.050000011920929*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 23.615355243633832*${_u_distance} variable xmax_converted equal 23.615355243633832*1 variable ymin_converted equal -47.23476048727959*${_u_distance} variable ymin_converted equal -47.23476048727959*1 variable ymax_converted equal 47.23476048727959*${_u_distance} variable ymax_converted equal 47.23476048727959*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050000011920929*${_u_distance} variable zmax_converted equal 4.050000011920929*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000001192093 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 23.6153552436338 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 23.6153552436338 -47.2347604872796 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 23.6153552436338 -47.2347604872796 47.2347604872796 ${zmin_converted} ${zmax_converted} units box region whole block 0 23.6153552436338 -47.2347604872796 47.2347604872796 0 ${zmax_converted} units box region whole block 0 23.6153552436338 -47.2347604872796 47.2347604872796 0 4.05000001192093 units box create_box 2 whole Created orthogonal box = (0 -47.2348 0) to (23.6154 47.2348 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 47.2347604872796 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -3 0 orient y 3 5 0 orient z 0 0 1 lattice fcc 4.05000001192093 orient x 5 -3 0 orient y 3 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.55655 5.55655 4.05 create_atoms 1 region upper Created 273 atoms create_atoms CPU = 0.000225067 secs group upper type 1 273 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.623928352680385 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -47.2347604872796 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 3 0 orient y -3 5 0 orient z 0 0 1 lattice fcc 4.05000001192093 orient x 5 3 0 orient y -3 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.55655 5.55655 4.05 create_atoms 2 region lower Created 273 atoms create_atoms CPU = 0.000131845 secs group lower type 2 273 atoms in group lower displace_atoms lower move -2.623928352680385 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_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*4.05000001192093 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500000596046 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, 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: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 536 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1787.6488 0 -1787.6488 -2510.9367 271 0 -1795.023 0 -1795.023 -6143.5381 Loop time of 1.26189 on 1 procs for 271 steps with 536 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 = -1787.64879815 -1795.0229901 -1795.0229901 Force two-norm initial, final = 7.83645 6.84246e-06 Force max component initial, final = 2.11805 9.6112e-07 Final line search alpha, max atom move = 1 9.6112e-07 Iterations, force evaluations = 271 522 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2296 | 1.2296 | 1.2296 | 0.0 | 97.44 Neigh | 0.0069408 | 0.0069408 | 0.0069408 | 0.0 | 0.55 Comm | 0.017301 | 0.017301 | 0.017301 | 0.0 | 1.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008069 | | | 0.64 Nlocal: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5428 ave 5428 max 5428 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: 92604 ave 92604 max 92604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92604 Ave neighs/atom = 172.769 Neighbor list builds = 3 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) = 4.526 | 4.526 | 4.526 Mbytes Step Temp E_pair E_mol TotEng Press Volume 271 0 -1795.023 0 -1795.023 -6143.5381 9035.2718 558 0 -1795.1373 0 -1795.1373 -869.20542 8974.2889 Loop time of 1.20439 on 1 procs for 287 steps with 536 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1795.0229901 -1795.13731835 -1795.13731835 Force two-norm initial, final = 47.2607 0.000295358 Force max component initial, final = 34.8867 8.59702e-05 Final line search alpha, max atom move = 0.958892 8.24361e-05 Iterations, force evaluations = 287 571 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.144 | 1.144 | 1.144 | 0.0 | 94.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014705 | 0.014705 | 0.014705 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04565 | | | 3.79 Nlocal: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5264 ave 5264 max 5264 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: 92624 ave 92624 max 92624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92624 Ave neighs/atom = 172.806 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 -0.00607941459516994 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 4.663 | 4.663 | 4.663 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1795.1373 0 -1795.1373 -869.20542 Loop time of 9.53674e-07 on 1 procs for 0 steps with 536 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: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5296 ave 5296 max 5296 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: 92740 ave 92740 max 92740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92740 Ave neighs/atom = 173.022 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) = 4.663 | 4.663 | 4.663 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 -1795.1373 -1795.1373 23.549188 94.469521 4.0339676 -869.20542 -869.20542 0.015305228 -2607.63 -0.0015710911 2.5323313 406.0675 Loop time of 9.53674e-07 on 1 procs for 0 steps with 536 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: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5296 ave 5296 max 5296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46370 ave 46370 max 46370 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 92740 ave 92740 max 92740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92740 Ave neighs/atom = 173.022 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_061.9275/numatoms.out 536 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1795.13731834613-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1795.13731834613-536*${isolated_atom_energy} variable adjusted_pe_metal equal -1795.13731834613-536*-0.00607941459516994 print "${adjusted_pe_metal} eV" file output/dump_061.9275/energy.out -1791.87875212312 eV print "${mindist_metal} Angstroms" file output/dump_061.9275/mindistance.out 2.53233126768936 Angstroms write_dump all cfg output/dump_061.9275/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_061.9275/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:02