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 4.210718545317654*${_u_distance} variable lattice_constant_converted equal 4.210718545317654*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 39.72383930892758*${_u_distance} variable xmax_converted equal 39.72383930892758*1 variable ymin_converted equal -79.45188933640048*${_u_distance} variable ymin_converted equal -79.45188933640048*1 variable ymax_converted equal 79.45188933640048*${_u_distance} variable ymax_converted equal 79.45188933640048*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.210718545317654*${_u_distance} variable zmax_converted equal 4.210718545317654*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.21071854531765 Lattice spacing in x,y,z = 4.21072 4.21072 4.21072 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 39.7238393089276 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.7238393089276 -79.4518893364005 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 39.7238393089276 -79.4518893364005 79.4518893364005 ${zmin_converted} ${zmax_converted} units box region whole block 0 39.7238393089276 -79.4518893364005 79.4518893364005 0 ${zmax_converted} units box region whole block 0 39.7238393089276 -79.4518893364005 79.4518893364005 0 4.21071854531765 units box create_box 2 whole Created orthogonal box = (0 -79.4519 0) to (39.7238 79.4519 4.21072) 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 79.4518893364005 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 -5 0 orient y 5 8 0 orient z 0 0 1 lattice fcc 4.21071854531765 orient x 8 -5 0 orient y 5 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.80236 5.80236 4.21072 create_atoms 1 region upper Created 714 atoms create_atoms CPU = 0.000325203 secs group upper type 1 714 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.245291509425472 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -79.4518893364005 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 5 0 orient y -5 8 0 orient z 0 0 1 lattice fcc 4.21071854531765 orient x 8 5 0 orient y -5 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.80236 5.80236 4.21072 create_atoms 2 region lower Created 714 atoms create_atoms CPU = 0.000134945 secs group lower type 2 714 atoms in group lower displace_atoms lower move -4.245291509425472 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SchopfBrommerFrigan_2012_AlMnPd__MO_137572817842_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*4.21071854531765 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.10535927265882 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1412 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.529 | 5.529 | 5.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5244.9392 0 -5244.9392 1301.9162 327 0 -5257.6583 0 -5257.6583 -1364.3352 Loop time of 3.58878 on 1 procs for 327 steps with 1412 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 = -5244.93921461 -5257.65829431 -5257.65829431 Force two-norm initial, final = 21.3586 1.87065e-05 Force max component initial, final = 5.46635 3.46362e-06 Final line search alpha, max atom move = 1 3.46362e-06 Iterations, force evaluations = 327 640 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5146 | 3.5146 | 3.5146 | 0.0 | 97.93 Neigh | 0.016151 | 0.016151 | 0.016151 | 0.0 | 0.45 Comm | 0.037669 | 0.037669 | 0.037669 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02031 | | | 0.57 Nlocal: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10065 ave 10065 max 10065 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: 244368 ave 244368 max 244368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 244368 Ave neighs/atom = 173.065 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) = 5.537 | 5.537 | 5.537 Mbytes Step Temp E_pair E_mol TotEng Press Volume 327 0 -5257.6583 0 -5257.6583 -1364.3352 26579.185 1327 0 -5257.6881 0 -5257.6881 -225.1453 26501.885 Loop time of 11.4292 on 1 procs for 1000 steps with 1412 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 = -5257.65829431 -5257.68805789 -5257.68805793 Force two-norm initial, final = 29.0423 0.0130917 Force max component initial, final = 20.9318 0.00744003 Final line search alpha, max atom move = 0.216505 0.0016108 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.93 | 10.93 | 10.93 | 0.0 | 95.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.117 | 0.117 | 0.117 | 0.0 | 1.02 Output | 1.812e-05 | 1.812e-05 | 1.812e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3823 | | | 3.35 Nlocal: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11089 ave 11089 max 11089 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: 244656 ave 244656 max 244656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 244656 Ave neighs/atom = 173.269 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 -0.09604918 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.675 | 5.675 | 5.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5257.6881 0 -5257.6881 -225.1453 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1412 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: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11098 ave 11098 max 11098 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: 244904 ave 244904 max 244904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 244904 Ave neighs/atom = 173.445 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) = 5.675 | 5.675 | 5.675 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 -5257.6881 -5257.6881 39.666265 158.90378 4.2045665 -225.1453 -225.1453 -0.36076021 -674.62602 -0.44913098 2.7487965 853.33939 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1412 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: 1412 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11098 ave 11098 max 11098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122452 ave 122452 max 122452 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 244904 ave 244904 max 244904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 244904 Ave neighs/atom = 173.445 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_064.0108/numatoms.out 1412 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5257.68805792829-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5257.68805792829-1412*${isolated_atom_energy} variable adjusted_pe_metal equal -5257.68805792829-1412*-0.09604918 print "${adjusted_pe_metal} eV" file output/dump_064.0108/energy.out -5122.06661576829 eV print "${mindist_metal} Angstroms" file output/dump_064.0108/mindistance.out 2.74879647443058 Angstroms write_dump all cfg output/dump_064.0108/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_064.0108/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15