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 4.032073378562927*${_u_distance} variable lattice_constant_converted equal 4.032073378562927*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 9.01599016473395*${_u_distance} variable xmax_converted equal 9.01599016473395*1 variable ymin_converted equal -45.08398289704831*${_u_distance} variable ymin_converted equal -45.08398289704831*1 variable ymax_converted equal 45.08398289704831*${_u_distance} variable ymax_converted equal 45.08398289704831*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032073378562927*${_u_distance} variable zmax_converted equal 4.032073378562927*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03207337856293 Lattice spacing in x,y,z = 4.03207 4.03207 4.03207 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 9.01599016473395 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 9.01599016473395 -45.0839828970483 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 9.01599016473395 -45.0839828970483 45.0839828970483 ${zmin_converted} ${zmax_converted} units box region whole block 0 9.01599016473395 -45.0839828970483 45.0839828970483 0 ${zmax_converted} units box region whole block 0 9.01599016473395 -45.0839828970483 45.0839828970483 0 4.03207337856293 units box create_box 2 whole Created orthogonal box = (0 -45.084 0) to (9.01599 45.084 4.03207) 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 45.0839828970483 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 lattice fcc 4.03207337856293 orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.40959 5.40959 4.03207 create_atoms 1 region upper Created 102 atoms create_atoms CPU = 0.000196934 secs group upper type 1 102 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.0062305898749053 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.0839828970483 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 lattice fcc 4.03207337856293 orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.40959 5.40959 4.03207 create_atoms 2 region lower Created 102 atoms create_atoms CPU = 5.29289e-05 secs group lower type 2 102 atoms in group lower displace_atoms lower move -1.0062305898749053 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_LiuLiuBorucki_1999_AlCu__MO_020851069572_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*4.03207337856293 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01603668928146 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 = 3 24 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 8 atoms, new total = 196 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 = 3 24 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) = 4.416 | 4.416 | 4.416 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -652.96865 0 -652.96865 -920.99751 221 0 -656.27557 0 -656.27557 -8432.304 Loop time of 0.260568 on 1 procs for 221 steps with 196 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 = -652.968649374 -656.275566926 -656.275566926 Force two-norm initial, final = 9.08908 7.48009e-07 Force max component initial, final = 3.66113 1.39957e-07 Final line search alpha, max atom move = 1 1.39957e-07 Iterations, force evaluations = 221 437 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25049 | 0.25049 | 0.25049 | 0.0 | 96.13 Neigh | 0.00068116 | 0.00068116 | 0.00068116 | 0.0 | 0.26 Comm | 0.0068133 | 0.0068133 | 0.0068133 | 0.0 | 2.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002583 | | | 0.99 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2854 ave 2854 max 2854 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: 25220 ave 25220 max 25220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25220 Ave neighs/atom = 128.673 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) = 4.416 | 4.416 | 4.416 Mbytes Step Temp E_pair E_mol TotEng Press Volume 221 0 -656.27557 0 -656.27557 -8432.304 3277.8881 1221 0 -656.35159 0 -656.35159 -1296.7783 3247.8589 Loop time of 1.22797 on 1 procs for 1000 steps with 196 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -656.275566926 -656.351590359 -656.351590359 Force two-norm initial, final = 23.2804 6.60213e-09 Force max component initial, final = 16.7796 5.50278e-09 Final line search alpha, max atom move = 1 5.50278e-09 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.115 | 1.115 | 1.115 | 0.0 | 90.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.028529 | 0.028529 | 0.028529 | 0.0 | 2.32 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08438 | | | 6.87 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2799 ave 2799 max 2799 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: 25536 ave 25536 max 25536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25536 Ave neighs/atom = 130.286 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 = 3 24 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) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -656.35159 0 -656.35159 -1296.7783 Loop time of 9.53674e-07 on 1 procs for 0 steps with 196 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: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2809 ave 2809 max 2809 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: 25568 ave 25568 max 25568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25568 Ave neighs/atom = 130.449 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) = 4.553 | 4.553 | 4.553 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 -656.35159 -656.35159 8.9763469 90.167966 4.0127791 -1296.7783 -1296.7783 1.6897207e-06 -3890.3349 2.7015449e-06 2.607102 193.0415 Loop time of 9.53674e-07 on 1 procs for 0 steps with 196 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: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2809 ave 2809 max 2809 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12784 ave 12784 max 12784 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25568 ave 25568 max 25568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25568 Ave neighs/atom = 130.449 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_053.1301/numatoms.out 196 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -656.351590358974-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -656.351590358974-196*${isolated_atom_energy} variable adjusted_pe_metal equal -656.351590358974-196*0 print "${adjusted_pe_metal} eV" file output/dump_053.1301/energy.out -656.351590358974 eV print "${mindist_metal} Angstroms" file output/dump_053.1301/mindistance.out 2.60710204106278 Angstroms write_dump all cfg output/dump_053.1301/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_053.1301/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:01