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 4.05000014603138*${_u_distance} variable lattice_constant_converted equal 4.05000014603138*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 34.60321641622866*${_u_distance} variable xmax_converted equal 34.60321641622866*1 variable ymin_converted equal -69.21048283260336*${_u_distance} variable ymin_converted equal -69.21048283260336*1 variable ymax_converted equal 69.21048283260336*${_u_distance} variable ymax_converted equal 69.21048283260336*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.05000014603138*${_u_distance} variable zmax_converted equal 4.05000014603138*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000014603138 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 34.6032164162287 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.6032164162287 -69.2104828326034 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.6032164162287 -69.2104828326034 69.2104828326034 ${zmin_converted} ${zmax_converted} units box region whole block 0 34.6032164162287 -69.2104828326034 69.2104828326034 0 ${zmax_converted} units box region whole block 0 34.6032164162287 -69.2104828326034 69.2104828326034 0 4.05000014603138 units box create_box 2 whole Created orthogonal box = (0 -69.2105 0) to (34.6032 69.2105 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 69.2104828326034 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 -3 0 orient y 3 8 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 8 -3 0 orient y 3 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.21418 5.21418 4.05 create_atoms 1 region upper Created 586 atoms create_atoms CPU = 0.000216007 secs group upper type 1 586 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.844801685392889 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -69.2104828326034 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 3 0 orient y -3 8 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 8 3 0 orient y -3 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.21418 5.21418 4.05 create_atoms 2 region lower Created 586 atoms create_atoms CPU = 0.000102043 secs group lower type 2 586 atoms in group lower displace_atoms lower move -3.844801685392889 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_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*4.05000014603138 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500007301569 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 9 33 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 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1154 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 9 33 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.068 | 5.068 | 5.068 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3859.9943 0 -3859.9943 -2017.552 229 0 -3867.8016 0 -3867.8016 -6181.8792 Loop time of 2.05664 on 1 procs for 229 steps with 1154 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3859.99431894 -3867.80163115 -3867.80163115 Force two-norm initial, final = 8.13807 6.03385e-06 Force max component initial, final = 2.29833 1.50821e-06 Final line search alpha, max atom move = 1 1.50821e-06 Iterations, force evaluations = 229 451 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0184 | 2.0184 | 2.0184 | 0.0 | 98.14 Neigh | 0.0045161 | 0.0045161 | 0.0045161 | 0.0 | 0.22 Comm | 0.021579 | 0.021579 | 0.021579 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01215 | | | 0.59 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8496 ave 8496 max 8496 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: 161904 ave 161904 max 161904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161904 Ave neighs/atom = 140.298 Neighbor list builds = 1 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) = 5.071 | 5.071 | 5.071 Mbytes Step Temp E_pair E_mol TotEng Press Volume 229 0 -3867.8016 0 -3867.8016 -6181.8792 19398.734 1229 0 -3868.0125 0 -3868.0125 -1259.8277 19277.083 Loop time of 9.15037 on 1 procs for 1000 steps with 1154 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 = -3867.80163115 -3868.0124858 -3868.01248587 Force two-norm initial, final = 94.1388 0.027648 Force max component initial, final = 69.5475 0.0153117 Final line search alpha, max atom move = 0.0562743 0.000861658 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7496 | 8.7496 | 8.7496 | 0.0 | 95.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.092369 | 0.092369 | 0.092369 | 0.0 | 1.01 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3084 | | | 3.37 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8826 ave 8826 max 8826 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: 161936 ave 161936 max 161936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161936 Ave neighs/atom = 140.326 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 0.0 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 9 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 5.209 | 5.209 | 5.209 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3868.0125 0 -3868.0125 -1259.8277 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1154 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: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8863 ave 8863 max 8863 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: 162232 ave 162232 max 162232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162232 Ave neighs/atom = 140.582 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) = 5.209 | 5.209 | 5.209 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 -3868.0125 -3868.0125 34.512597 138.42097 4.0351696 -1259.8277 -1259.8277 0.90572035 -3781.6568 1.2679451 2.5634824 581.74524 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1154 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 | | 2.146e-06 | | |100.00 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8863 ave 8863 max 8863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81116 ave 81116 max 81116 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 162232 ave 162232 max 162232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162232 Ave neighs/atom = 140.582 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_041.1121/numatoms.out 1154 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3868.0124858713-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3868.0124858713-1154*${isolated_atom_energy} variable adjusted_pe_metal equal -3868.0124858713-1154*0 print "${adjusted_pe_metal} eV" file output/dump_041.1121/energy.out -3868.0124858713 eV print "${mindist_metal} Angstroms" file output/dump_041.1121/mindistance.out 2.56348244425591 Angstroms write_dump all cfg output/dump_041.1121/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_041.1121/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:11