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 4.03203821182251*${_u_distance} variable lattice_constant_converted equal 4.03203821182251*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 66.13034361085353*${_u_distance} variable xmax_converted equal 66.13034361085353*1 variable ymin_converted equal -66.13437564906535*${_u_distance} variable ymin_converted equal -66.13437564906535*1 variable ymax_converted equal 66.13437564906535*${_u_distance} variable ymax_converted equal 66.13437564906535*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.03203821182251*${_u_distance} variable zmax_converted equal 4.03203821182251*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03203821182251 Lattice spacing in x,y,z = 4.03204 4.03204 4.03204 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 66.1303436108535 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 66.1303436108535 -66.1343756490653 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 66.1303436108535 -66.1343756490653 66.1343756490653 ${zmin_converted} ${zmax_converted} units box region whole block 0 66.1303436108535 -66.1343756490653 66.1343756490653 0 ${zmax_converted} units box region whole block 0 66.1303436108535 -66.1343756490653 66.1343756490653 0 4.03203821182251 units box create_box 2 whole Created orthogonal box = (0 -66.1344 0) to (66.1303 66.1344 4.03204) 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 66.1343756490653 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -10 0 orient y 10 13 0 orient z 0 0 1 lattice fcc 4.03203821182251 orient x 13 -10 0 orient y 10 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.65427 5.65427 4.03204 create_atoms 1 region upper Created 1078 atoms create_atoms CPU = 0.000287056 secs group upper type 1 1078 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.380548760085527 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -66.1343756490653 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 10 0 orient y -10 13 0 orient z 0 0 1 lattice fcc 4.03203821182251 orient x 13 10 0 orient y -10 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.65427 5.65427 4.03204 create_atoms 2 region lower Created 1078 atoms create_atoms CPU = 0.000181913 secs group lower type 2 1078 atoms in group lower displace_atoms lower move -7.380548760085527 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_LiuAdams_1998_AlMg__MO_019873715786_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*4.03203821182251 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01601910591125 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 16 31 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2128 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 16 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.052 | 6.052 | 6.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7099.6155 0 -7099.6155 1500.6806 572 0 -7131.3976 0 -7131.3976 -4628.7306 Loop time of 8.92549 on 1 procs for 572 steps with 2128 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 = -7099.61553396 -7131.39758018 -7131.39758018 Force two-norm initial, final = 34.6396 1.0326e-06 Force max component initial, final = 8.32526 2.72735e-07 Final line search alpha, max atom move = 1 2.72735e-07 Iterations, force evaluations = 572 1120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7302 | 8.7302 | 8.7302 | 0.0 | 97.81 Neigh | 0.052982 | 0.052982 | 0.052982 | 0.0 | 0.59 Comm | 0.09209 | 0.09209 | 0.09209 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05023 | | | 0.56 Nlocal: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14530 ave 14530 max 14530 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: 368512 ave 368512 max 368512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368512 Ave neighs/atom = 173.173 Neighbor list builds = 6 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) = 9.569 | 9.569 | 9.569 Mbytes Step Temp E_pair E_mol TotEng Press Volume 572 0 -7131.3976 0 -7131.3976 -4628.7306 35268.149 1572 0 -7131.6415 0 -7131.6415 -952.67682 35109.75 Loop time of 16.7377 on 1 procs for 1000 steps with 2128 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 = -7131.39758018 -7131.64152876 -7131.64152934 Force two-norm initial, final = 135.207 0.100162 Force max component initial, final = 114.712 0.0935466 Final line search alpha, max atom move = 0.0161736 0.00151298 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.063 | 16.063 | 16.063 | 0.0 | 95.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15433 | 0.15433 | 0.15433 | 0.0 | 0.92 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5204 | | | 3.11 Nlocal: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14524 ave 14524 max 14524 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: 368820 ave 368820 max 368820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368820 Ave neighs/atom = 173.318 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 16 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 9.332 | 9.332 | 9.332 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7131.6415 0 -7131.6415 -952.67682 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2128 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: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14547 ave 14547 max 14547 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: 369128 ave 369128 max 369128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369128 Ave neighs/atom = 173.462 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) = 9.332 | 9.332 | 9.332 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 -7131.6415 -7131.6415 65.884529 132.26875 4.028905 -952.67682 -952.67682 0.38730229 -2862.6833 4.2655299 2.5055914 957.57449 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2128 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: 2128 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14547 ave 14547 max 14547 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 184564 ave 184564 max 184564 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 369128 ave 369128 max 369128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369128 Ave neighs/atom = 173.462 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_075.1372/numatoms.out 2128 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7131.64152934292-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7131.64152934292-2128*${isolated_atom_energy} variable adjusted_pe_metal equal -7131.64152934292-2128*0 print "${adjusted_pe_metal} eV" file output/dump_075.1372/energy.out -7131.64152934292 eV print "${mindist_metal} Angstroms" file output/dump_075.1372/mindistance.out 2.50559140874662 Angstroms write_dump all cfg output/dump_075.1372/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_075.1372/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:25