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 4.049763545393944*${_u_distance} variable lattice_constant_converted equal 4.049763545393944*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 80.38551113726328*${_u_distance} variable xmax_converted equal 80.38551113726328*1 variable ymin_converted equal -80.38956090080868*${_u_distance} variable ymin_converted equal -80.38956090080868*1 variable ymax_converted equal 80.38956090080868*${_u_distance} variable ymax_converted equal 80.38956090080868*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049763545393944*${_u_distance} variable zmax_converted equal 4.049763545393944*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04976354539394 Lattice spacing in x,y,z = 4.04976 4.04976 4.04976 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 80.3855111372633 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 80.3855111372633 -80.3895609008087 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 80.3855111372633 -80.3895609008087 80.3895609008087 ${zmin_converted} ${zmax_converted} units box region whole block 0 80.3855111372633 -80.3895609008087 80.3895609008087 0 ${zmax_converted} units box region whole block 0 80.3855111372633 -80.3895609008087 80.3895609008087 0 4.04976354539394 units box create_box 2 whole Created orthogonal box = (0 -80.3896 0) to (80.3855 80.3896 4.04976) 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 80.3895609008087 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 lattice fcc 4.04976354539394 orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71268 5.71268 4.04976 create_atoms 1 region upper Created 1577 atoms create_atoms CPU = 0.000540972 secs group upper type 1 1577 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.932244958575643 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -80.3895609008087 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 lattice fcc 4.04976354539394 orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71268 5.71268 4.04976 create_atoms 2 region lower Created 1577 atoms create_atoms CPU = 0.000453949 secs group lower type 2 1577 atoms in group lower displace_atoms lower move -8.932244958575643 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_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*4.04976354539394 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02488177269697 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 19 38 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 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 35 atoms, new total = 3119 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 19 38 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.93 | 10.93 | 10.93 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10313.432 0 -10313.432 -696.53458 135 0 -10337.8 0 -10337.8 -6216.1515 Loop time of 2.99866 on 1 procs for 135 steps with 3119 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -10313.4315169 -10337.7996766 -10337.7996766 Force two-norm initial, final = 18.0894 0.017001 Force max component initial, final = 4.91657 0.00480525 Final line search alpha, max atom move = 3.05176e-05 1.46644e-07 Iterations, force evaluations = 135 271 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9155 | 2.9155 | 2.9155 | 0.0 | 97.23 Neigh | 0.040352 | 0.040352 | 0.040352 | 0.0 | 1.35 Comm | 0.026338 | 0.026338 | 0.026338 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01648 | | | 0.55 Nlocal: 3119 ave 3119 max 3119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17881 ave 17881 max 17881 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: 535338 ave 535338 max 535338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 535338 Ave neighs/atom = 171.638 Neighbor list builds = 4 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) = 10.93 | 10.93 | 10.93 Mbytes Step Temp E_pair E_mol TotEng Press Volume 135 0 -10337.8 0 -10337.8 -6216.1515 52340.407 164 0 -10338.37 0 -10338.37 -1456.4265 52009.364 Loop time of 1.10634 on 1 procs for 29 steps with 3119 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -10337.7996766 -10338.3701203 -10338.3701203 Force two-norm initial, final = 230.774 0.268711 Force max component initial, final = 179.781 0.25203 Final line search alpha, max atom move = 9.47526e-08 2.38805e-08 Iterations, force evaluations = 29 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0694 | 1.0694 | 1.0694 | 0.0 | 96.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0081325 | 0.0081325 | 0.0081325 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02877 | | | 2.60 Nlocal: 3119 ave 3119 max 3119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17891 ave 17891 max 17891 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: 534946 ave 534946 max 534946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 534946 Ave neighs/atom = 171.512 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 19 38 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 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) = 10.44 | 10.44 | 10.44 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10338.37 0 -10338.37 -1456.4265 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3119 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: 3119 ave 3119 max 3119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17891 ave 17891 max 17891 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: 536190 ave 536190 max 536190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536190 Ave neighs/atom = 171.911 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) = 10.44 | 10.44 | 10.44 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 -10338.37 -10338.37 80.38048 160.77912 4.0244015 -1456.4265 -1456.4265 1.8924258 -4378.8873 7.7153067 2.5320404 519.97973 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3119 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: 3119 ave 3119 max 3119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17891 ave 17891 max 17891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 268095 ave 268095 max 268095 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 536190 ave 536190 max 536190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536190 Ave neighs/atom = 171.911 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_081.8288/numatoms.out 3119 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -10338.3701202847-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -10338.3701202847-3119*${isolated_atom_energy} variable adjusted_pe_metal equal -10338.3701202847-3119*0 print "${adjusted_pe_metal} eV" file output/dump_081.8288/energy.out -10338.3701202847 eV print "${mindist_metal} Angstroms" file output/dump_081.8288/mindistance.out 2.53204040404066 Angstroms write_dump all cfg output/dump_081.8288/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_081.8288/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:04