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 4.050010219216347*${_u_distance} variable lattice_constant_converted equal 4.050010219216347*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 20.250051096081734*${_u_distance} variable xmax_converted equal 20.250051096081734*1 variable ymin_converted equal -40.504152202382684*${_u_distance} variable ymin_converted equal -40.504152202382684*1 variable ymax_converted equal 40.504152202382684*${_u_distance} variable ymax_converted equal 40.504152202382684*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050010219216347*${_u_distance} variable zmax_converted equal 4.050010219216347*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05001021921635 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 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 20.2500510960817 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 20.2500510960817 -40.5041522023827 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 20.2500510960817 -40.5041522023827 40.5041522023827 ${zmin_converted} ${zmax_converted} units box region whole block 0 20.2500510960817 -40.5041522023827 40.5041522023827 0 ${zmax_converted} units box region whole block 0 20.2500510960817 -40.5041522023827 40.5041522023827 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -40.5042 0) to (20.2501 40.5042 4.05001) 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 40.5041522023827 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 -3 0 orient y 3 4 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 4 -3 0 orient y 3 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67001 5.67001 4.05001 create_atoms 1 region upper Created 202 atoms create_atoms CPU = 0.000174046 secs group upper type 1 202 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.25 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -40.5041522023827 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 3 0 orient y -3 4 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 4 3 0 orient y -3 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67001 5.67001 4.05001 create_atoms 2 region lower Created 202 atoms create_atoms CPU = 4.91142e-05 secs group lower type 2 202 atoms in group lower displace_atoms lower move -2.25 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_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*4.05001021921635 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500510960818 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 6 22 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 392 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.453 | 4.453 | 4.453 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1314.3807 0 -1314.3807 2065.3953 229 0 -1322.9001 0 -1322.9001 -8999.2346 Loop time of 0.436852 on 1 procs for 229 steps with 392 atoms 100.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1314.38073135 -1322.90010588 -1322.90010588 Force two-norm initial, final = 16.762 1.06675e-05 Force max component initial, final = 5.21388 2.83074e-06 Final line search alpha, max atom move = 1 2.83074e-06 Iterations, force evaluations = 229 449 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42307 | 0.42307 | 0.42307 | 0.0 | 96.85 Neigh | 0.00089407 | 0.00089407 | 0.00089407 | 0.0 | 0.20 Comm | 0.0085492 | 0.0085492 | 0.0085492 | 0.0 | 1.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004336 | | | 0.99 Nlocal: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3708 ave 3708 max 3708 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: 40836 ave 40836 max 40836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40836 Ave neighs/atom = 104.173 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) = 4.453 | 4.453 | 4.453 Mbytes Step Temp E_pair E_mol TotEng Press Volume 229 0 -1322.9001 0 -1322.9001 -8999.2346 6643.7271 1229 0 -1323.0428 0 -1323.0428 -2392.412 6584.6143 Loop time of 2.23883 on 1 procs for 1000 steps with 392 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1322.90010588 -1323.04281462 -1323.04281462 Force two-norm initial, final = 41.7157 0.00156968 Force max component initial, final = 32.2659 0.00115623 Final line search alpha, max atom move = 1 0.00115623 Iterations, force evaluations = 1000 1993 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0657 | 2.0657 | 2.0657 | 0.0 | 92.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.040169 | 0.040169 | 0.040169 | 0.0 | 1.79 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.133 | | | 5.94 Nlocal: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3708 ave 3708 max 3708 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: 40024 ave 40024 max 40024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40024 Ave neighs/atom = 102.102 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 6 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1323.0428 0 -1323.0428 -2392.412 Loop time of 9.53674e-07 on 1 procs for 0 steps with 392 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: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3708 ave 3708 max 3708 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: 44072 ave 44072 max 44072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44072 Ave neighs/atom = 112.429 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) = 4.591 | 4.591 | 4.591 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 -1323.0428 -1323.0428 20.237983 81.008304 4.0163688 -2392.412 -2392.412 0.25432567 -7177.2113 -0.2789983 2.5404852 266.15418 Loop time of 9.53674e-07 on 1 procs for 0 steps with 392 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: 392 ave 392 max 392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3708 ave 3708 max 3708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22036 ave 22036 max 22036 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44072 ave 44072 max 44072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44072 Ave neighs/atom = 112.429 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_073.7398/numatoms.out 392 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1323.04281461744-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1323.04281461744-392*${isolated_atom_energy} variable adjusted_pe_metal equal -1323.04281461744-392*0 print "${adjusted_pe_metal} eV" file output/dump_073.7398/energy.out -1323.04281461744 eV print "${mindist_metal} Angstroms" file output/dump_073.7398/mindistance.out 2.540485248558 Angstroms write_dump all cfg output/dump_073.7398/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_073.7398/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:02