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 48.76845818765579*${_u_distance} variable xmax_converted equal 48.76845818765579*1 variable ymin_converted equal -48.77250818766771*${_u_distance} variable ymin_converted equal -48.77250818766771*1 variable ymax_converted equal 48.77250818766771*${_u_distance} variable ymax_converted equal 48.77250818766771*1 variable zmin_converted equal 0.0*${_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 48.7684581876558 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 48.7684581876558 -48.7725081876677 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 48.7684581876558 -48.7725081876677 48.7725081876677 ${zmin_converted} ${zmax_converted} units box region whole block 0 48.7684581876558 -48.7725081876677 48.7725081876677 0 ${zmax_converted} units box region whole block 0 48.7684581876558 -48.7725081876677 48.7725081876677 0 4.05000001192093 units box create_box 2 whole Created orthogonal box = (0 -48.7725 0) to (48.7685 48.7725 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 48.7725081876677 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -1 0 orient y 1 12 0 orient z 0 0 1 lattice fcc 4.05000001192093 orient x 12 -1 0 orient y 1 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.37234 4.37234 4.05 create_atoms 1 region upper Created 582 atoms create_atoms CPU = 0.000262022 secs group upper type 1 582 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.418717560456534 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -48.7725081876677 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 1 0 orient y -1 12 0 orient z 0 0 1 lattice fcc 4.05000001192093 orient x 12 1 0 orient y -1 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.37234 4.37234 4.05 create_atoms 2 region lower Created 582 atoms create_atoms CPU = 0.000123978 secs group lower type 2 582 atoms in group lower displace_atoms lower move -5.418717560456534 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 12 23 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 22 atoms, new total = 1142 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 = 12 23 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) = 5.429 | 5.429 | 5.429 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3818.9232 0 -3818.9232 -2772.302 239 0 -3826.6699 0 -3826.6699 -7929.7097 Loop time of 2.3496 on 1 procs for 239 steps with 1142 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3818.92321667 -3826.66985371 -3826.66985371 Force two-norm initial, final = 7.3715 5.74254e-07 Force max component initial, final = 2.08502 6.51707e-08 Final line search alpha, max atom move = 1 6.51707e-08 Iterations, force evaluations = 239 471 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3158 | 2.3158 | 2.3158 | 0.0 | 98.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.021089 | 0.021089 | 0.021089 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01267 | | | 0.54 Nlocal: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7938 ave 7938 max 7938 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: 197328 ave 197328 max 197328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197328 Ave neighs/atom = 172.792 Neighbor list builds = 0 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) = 5.431 | 5.431 | 5.431 Mbytes Step Temp E_pair E_mol TotEng Press Volume 239 0 -3826.6699 0 -3826.6699 -7929.7097 19266.336 1239 0 -3826.9461 0 -3826.9461 -2349.9641 19127.419 Loop time of 10.0218 on 1 procs for 1000 steps with 1142 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 = -3826.66985371 -3826.9460702 -3826.94607022 Force two-norm initial, final = 107.324 0.00539893 Force max component initial, final = 78.0508 0.00333994 Final line search alpha, max atom move = 0.146144 0.000488113 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.6388 | 9.6388 | 9.6388 | 0.0 | 96.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.085914 | 0.085914 | 0.085914 | 0.0 | 0.86 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.297 | | | 2.96 Nlocal: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8200 ave 8200 max 8200 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: 196176 ave 196176 max 196176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196176 Ave neighs/atom = 171.783 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 = 12 23 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) = 5.57 | 5.57 | 5.57 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3826.9461 0 -3826.9461 -2349.9641 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1142 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: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8266 ave 8266 max 8266 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: 196768 ave 196768 max 196768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196768 Ave neighs/atom = 172.301 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) = 5.57 | 5.57 | 5.57 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 -3826.9461 -3826.9461 48.608941 97.545016 4.0339929 -2349.9641 -2349.9641 0.27884956 -7049.9952 -0.17595883 2.566002 351.95367 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1142 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: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8266 ave 8266 max 8266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98384 ave 98384 max 98384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 196768 ave 196768 max 196768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196768 Ave neighs/atom = 172.301 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_009.5273/numatoms.out 1142 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3826.9460702201-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3826.9460702201-1142*${isolated_atom_energy} variable adjusted_pe_metal equal -3826.9460702201-1142*-0.00607941459516994 print "${adjusted_pe_metal} eV" file output/dump_009.5273/energy.out -3820.00337875242 eV print "${mindist_metal} Angstroms" file output/dump_009.5273/mindistance.out 2.56600196488334 Angstroms write_dump all cfg output/dump_009.5273/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_009.5273/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:12