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 4.024845376610756*${_u_distance} variable lattice_constant_converted equal 4.024845376610756*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 30.65230917445289*${_u_distance} variable xmax_converted equal 30.65230917445289*1 variable ymin_converted equal -61.30864319428239*${_u_distance} variable ymin_converted equal -61.30864319428239*1 variable ymax_converted equal 61.30864319428239*${_u_distance} variable ymax_converted equal 61.30864319428239*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.024845376610756*${_u_distance} variable zmax_converted equal 4.024845376610756*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.02484537661076 Lattice spacing in x,y,z = 4.02485 4.02485 4.02485 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 30.6523091744529 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.6523091744529 -61.3086431942824 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.6523091744529 -61.3086431942824 61.3086431942824 ${zmin_converted} ${zmax_converted} units box region whole block 0 30.6523091744529 -61.3086431942824 61.3086431942824 0 ${zmax_converted} units box region whole block 0 30.6523091744529 -61.3086431942824 61.3086431942824 0 4.02484537661076 units box create_box 2 whole Created orthogonal box = (0 -61.3086 0) to (30.6523 61.3086 4.02485) 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 61.3086431942824 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -3 0 orient y 3 7 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 7 -3 0 orient y 3 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.28488 5.28488 4.02485 create_atoms 1 region upper Created 466 atoms create_atoms CPU = 0.000262976 secs group upper type 1 466 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.4270978976387587 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.3086431942824 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 3 0 orient y -3 7 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 7 3 0 orient y -3 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.28488 5.28488 4.02485 create_atoms 2 region lower Created 466 atoms create_atoms CPU = 0.000133038 secs group lower type 2 466 atoms in group lower displace_atoms lower move -3.4270978976387587 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_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*4.02484537661076 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01242268830538 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 30 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 916 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.009 | 5.009 | 5.009 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2408.7544 0 -2408.7544 -2404.2346 561 0 -2416.3765 0 -2416.3765 -5500.6347 Loop time of 3.40471 on 1 procs for 561 steps with 916 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2408.75436791 -2416.37647819 -2416.37647819 Force two-norm initial, final = 10.324 1.2542e-05 Force max component initial, final = 2.44936 2.54635e-06 Final line search alpha, max atom move = 1 2.54635e-06 Iterations, force evaluations = 561 1118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3306 | 3.3306 | 3.3306 | 0.0 | 97.82 Neigh | 0.006381 | 0.006381 | 0.006381 | 0.0 | 0.19 Comm | 0.043806 | 0.043806 | 0.043806 | 0.0 | 1.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02389 | | | 0.70 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7109 ave 7109 max 7109 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: 127780 ave 127780 max 127780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127780 Ave neighs/atom = 139.498 Neighbor list builds = 2 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) = 5.01 | 5.01 | 5.01 Mbytes Step Temp E_pair E_mol TotEng Press Volume 561 0 -2416.3765 0 -2416.3765 -5500.6347 15127.393 1561 0 -2416.5341 0 -2416.5341 -729.5125 15034.713 Loop time of 6.68475 on 1 procs for 1000 steps with 916 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 = -2416.37647819 -2416.53408019 -2416.53408022 Force two-norm initial, final = 71.2937 0.0214147 Force max component initial, final = 53.3606 0.0155357 Final line search alpha, max atom move = 0.322478 0.00500991 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3637 | 6.3637 | 6.3637 | 0.0 | 95.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.072974 | 0.072974 | 0.072974 | 0.0 | 1.09 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2481 | | | 3.71 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7109 ave 7109 max 7109 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: 127800 ave 127800 max 127800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127800 Ave neighs/atom = 139.52 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 -0.0307342631051472 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.147 | 5.147 | 5.147 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2416.5341 0 -2416.5341 -729.5125 Loop time of 0 on 1 procs for 0 steps with 916 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 | | 0 | | | 0.00 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7109 ave 7109 max 7109 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: 127824 ave 127824 max 127824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127824 Ave neighs/atom = 139.546 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) = 5.147 | 5.147 | 5.147 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 -2416.5341 -2416.5341 30.580457 122.61729 4.0095854 -729.5125 -729.5125 -1.6516803 -2185.4929 -1.3929091 2.5511192 545.97199 Loop time of 9.53674e-07 on 1 procs for 0 steps with 916 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: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7109 ave 7109 max 7109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63912 ave 63912 max 63912 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127824 ave 127824 max 127824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127824 Ave neighs/atom = 139.546 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_046.3972/numatoms.out 916 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2416.53408022135-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2416.53408022135-916*${isolated_atom_energy} variable adjusted_pe_metal equal -2416.53408022135-916*-0.0307342631051472 print "${adjusted_pe_metal} eV" file output/dump_046.3972/energy.out -2388.38149521704 eV print "${mindist_metal} Angstroms" file output/dump_046.3972/mindistance.out 2.55111919069759 Angstroms write_dump all cfg output/dump_046.3972/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_046.3972/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:10