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 4.031036108732224*${_u_distance} variable lattice_constant_converted equal 4.031036108732224*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 59.925659915336524*${_u_distance} variable xmax_converted equal 59.925659915336524*1 variable ymin_converted equal -59.92969095144526*${_u_distance} variable ymin_converted equal -59.92969095144526*1 variable ymax_converted equal 59.92969095144526*${_u_distance} variable ymax_converted equal 59.92969095144526*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.031036108732224*${_u_distance} variable zmax_converted equal 4.031036108732224*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03103610873222 Lattice spacing in x,y,z = 4.03104 4.03104 4.03104 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 59.9256599153365 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 59.9256599153365 -59.9296909514453 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 59.9256599153365 -59.9296909514453 59.9296909514453 ${zmin_converted} ${zmax_converted} units box region whole block 0 59.9256599153365 -59.9296909514453 59.9296909514453 0 ${zmax_converted} units box region whole block 0 59.9256599153365 -59.9296909514453 59.9296909514453 0 4.03103610873222 units box create_box 2 whole Created orthogonal box = (0 -59.9297 0) to (59.9257 59.9297 4.03104) 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 59.9296909514453 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -5 0 orient y 5 14 0 orient z 0 0 1 lattice fcc 4.03103610873222 orient x 14 -5 0 orient y 5 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.15198 5.15198 4.03104 create_atoms 1 region upper Created 885 atoms create_atoms CPU = 0.000324011 secs group upper type 1 885 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.689730936293327 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -59.9296909514453 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 5 0 orient y -5 14 0 orient z 0 0 1 lattice fcc 4.03103610873222 orient x 14 5 0 orient y -5 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.15198 5.15198 4.03104 create_atoms 2 region lower Created 885 atoms create_atoms CPU = 0.000201941 secs group lower type 2 885 atoms in group lower displace_atoms lower move -6.689730936293327 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_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*4.03103610873222 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01551805436611 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 16 32 2 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 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 1748 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 16 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.556 | 5.556 | 5.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5827.8788 0 -5827.8788 2198.1429 349 0 -5855.9958 0 -5855.9958 -4281.7209 Loop time of 2.99796 on 1 procs for 349 steps with 1748 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5827.87884941 -5855.99577751 -5855.99577751 Force two-norm initial, final = 30.6681 3.57595e-06 Force max component initial, final = 6.15092 1.15252e-06 Final line search alpha, max atom move = 1 1.15252e-06 Iterations, force evaluations = 349 680 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9296 | 2.9296 | 2.9296 | 0.0 | 97.72 Neigh | 0.004158 | 0.004158 | 0.004158 | 0.0 | 0.14 Comm | 0.039397 | 0.039397 | 0.039397 | 0.0 | 1.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02482 | | | 0.83 Nlocal: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10582 ave 10582 max 10582 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: 229018 ave 229018 max 229018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229018 Ave neighs/atom = 131.017 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) = 5.556 | 5.556 | 5.556 Mbytes Step Temp E_pair E_mol TotEng Press Volume 349 0 -5855.9958 0 -5855.9958 -4281.7209 28953.532 1349 0 -5856.1366 0 -5856.1366 -1093.9042 28827.447 Loop time of 9.01043 on 1 procs for 1000 steps with 1748 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 = -5855.99577751 -5856.13663709 -5856.13663712 Force two-norm initial, final = 91.3882 0.0147906 Force max component initial, final = 65.1256 0.00865826 Final line search alpha, max atom move = 0.171381 0.00148386 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.5194 | 8.5194 | 8.5194 | 0.0 | 94.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10753 | 0.10753 | 0.10753 | 0.0 | 1.19 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3835 | | | 4.26 Nlocal: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10607 ave 10607 max 10607 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: 229742 ave 229742 max 229742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229742 Ave neighs/atom = 131.431 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 16 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 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) = 5.694 | 5.694 | 5.694 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5856.1366 0 -5856.1366 -1093.9042 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1748 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: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10607 ave 10607 max 10607 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: 229848 ave 229848 max 229848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229848 Ave neighs/atom = 131.492 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) = 5.694 | 5.694 | 5.694 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 -5856.1366 -5856.1366 59.79759 119.85938 4.0220778 -1093.9042 -1093.9042 0.4801819 -3281.8629 -0.32987254 2.5101226 1119.5773 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1748 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: 1748 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10607 ave 10607 max 10607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114924 ave 114924 max 114924 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 229848 ave 229848 max 229848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229848 Ave neighs/atom = 131.492 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_039.3076/numatoms.out 1748 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5856.13663712431-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5856.13663712431-1748*${isolated_atom_energy} variable adjusted_pe_metal equal -5856.13663712431-1748*0 print "${adjusted_pe_metal} eV" file output/dump_039.3076/energy.out -5856.13663712431 eV print "${mindist_metal} Angstroms" file output/dump_039.3076/mindistance.out 2.5101225574483 Angstroms write_dump all cfg output/dump_039.3076/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_039.3076/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:12