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 42.86152794176955*${_u_distance} variable xmax_converted equal 42.86152794176955*1 variable ymin_converted equal -42.86556001514811*${_u_distance} variable ymin_converted equal -42.86556001514811*1 variable ymax_converted equal 42.86556001514811*${_u_distance} variable ymax_converted equal 42.86556001514811*1 variable zmin_converted equal 0.0*${_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 42.8615279417696 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.8615279417696 -42.8655600151481 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 42.8615279417696 -42.8655600151481 42.8655600151481 ${zmin_converted} ${zmax_converted} units box region whole block 0 42.8615279417696 -42.8655600151481 42.8655600151481 0 ${zmax_converted} units box region whole block 0 42.8615279417696 -42.8655600151481 42.8655600151481 0 4.03207337856293 units box create_box 2 whole Created orthogonal box = (0 -42.8656 0) to (42.8615 42.8656 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 42.8655600151481 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 -7 0 orient y 7 8 0 orient z 0 0 1 lattice fcc 4.03207337856293 orient x 8 -7 0 orient y 7 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68958 5.68958 4.03207 create_atoms 1 region upper Created 453 atoms create_atoms CPU = 0.00026989 secs group upper type 1 453 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.783565615730593 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -42.8655600151481 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 7 0 orient y -7 8 0 orient z 0 0 1 lattice fcc 4.03207337856293 orient x 8 7 0 orient y -7 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68958 5.68958 4.03207 create_atoms 2 region lower Created 453 atoms create_atoms CPU = 0.000149965 secs group lower type 2 453 atoms in group lower displace_atoms lower move -4.783565615730593 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 12 23 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 18 atoms, new total = 888 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 = 12 23 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) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2956.034 0 -2956.034 512.00465 232 0 -2973.328 0 -2973.328 -9082.3863 Loop time of 1.09337 on 1 procs for 232 steps with 888 atoms 100.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2956.03396335 -2973.32800519 -2973.32800519 Force two-norm initial, final = 21.6726 5.32934e-07 Force max component initial, final = 4.40136 1.01455e-07 Final line search alpha, max atom move = 1 1.01455e-07 Iterations, force evaluations = 232 452 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0683 | 1.0683 | 1.0683 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015704 | 0.015704 | 0.015704 | 0.0 | 1.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00933 | | | 0.85 Nlocal: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6212 ave 6212 max 6212 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: 115674 ave 115674 max 115674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115674 Ave neighs/atom = 130.264 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) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press Volume 232 0 -2973.328 0 -2973.328 -9082.3863 14816.123 1232 0 -2973.5706 0 -2973.5706 -3344.646 14708.677 Loop time of 4.69709 on 1 procs for 1000 steps with 888 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2973.32800519 -2973.57063986 -2973.57063991 Force two-norm initial, final = 87.9342 0.0222582 Force max component initial, final = 72.1697 0.0216949 Final line search alpha, max atom move = 0.248848 0.00539873 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4155 | 4.4155 | 4.4155 | 0.0 | 94.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.062649 | 0.062649 | 0.062649 | 0.0 | 1.33 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2189 | | | 4.66 Nlocal: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6131 ave 6131 max 6131 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: 113776 ave 113776 max 113776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113776 Ave neighs/atom = 128.126 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 = 12 23 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) = 5.091 | 5.091 | 5.091 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2973.5706 0 -2973.5706 -3344.646 Loop time of 9.53674e-07 on 1 procs for 0 steps with 888 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: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6149 ave 6149 max 6149 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: 114208 ave 114208 max 114208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114208 Ave neighs/atom = 128.613 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) = 5.091 | 5.091 | 5.091 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 -2973.5706 -2973.5706 42.63314 85.73112 4.0242764 -3344.646 -3344.646 2.3505753 -10035.95 -0.33870788 2.615985 268.03452 Loop time of 9.53674e-07 on 1 procs for 0 steps with 888 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: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6149 ave 6149 max 6149 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57104 ave 57104 max 57104 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114208 ave 114208 max 114208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114208 Ave neighs/atom = 128.613 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_082.3719/numatoms.out 888 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2973.57063991148-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2973.57063991148-888*${isolated_atom_energy} variable adjusted_pe_metal equal -2973.57063991148-888*0 print "${adjusted_pe_metal} eV" file output/dump_082.3719/energy.out -2973.57063991148 eV print "${mindist_metal} Angstroms" file output/dump_082.3719/mindistance.out 2.61598498377672 Angstroms write_dump all cfg output/dump_082.3719/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_082.3719/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:05