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 8.999827861027393*${_u_distance} variable xmax_converted equal 8.999827861027393*1 variable ymin_converted equal -45.00316415051358*${_u_distance} variable ymin_converted equal -45.00316415051358*1 variable ymax_converted equal 45.00316415051358*${_u_distance} variable ymax_converted equal 45.00316415051358*1 variable zmin_converted equal 0.0*${_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 8.99982786102739 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 8.99982786102739 -45.0031641505136 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 8.99982786102739 -45.0031641505136 45.0031641505136 ${zmin_converted} ${zmax_converted} units box region whole block 0 8.99982786102739 -45.0031641505136 45.0031641505136 0 ${zmax_converted} units box region whole block 0 8.99982786102739 -45.0031641505136 45.0031641505136 0 4.02484537661076 units box create_box 2 whole Created orthogonal box = (0 -45.0032 0) to (8.99983 45.0032 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 45.0031641505136 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 2 -1 0 orient y 1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.3999 5.3999 4.02485 create_atoms 1 region upper Created 102 atoms create_atoms CPU = 0.000190973 secs group upper type 1 102 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.0062305898749053 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.0031641505136 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 2 1 0 orient y -1 2 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.3999 5.3999 4.02485 create_atoms 2 region lower Created 102 atoms create_atoms CPU = 5.48363e-05 secs group lower type 2 102 atoms in group lower displace_atoms lower move -1.0062305898749053 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 3 22 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 8 atoms, new total = 196 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 = 3 22 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) = 4.437 | 4.437 | 4.437 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -513.46361 0 -513.46361 -4184.1648 190 0 -516.44688 0 -516.44688 -8361.8139 Loop time of 0.262946 on 1 procs for 190 steps with 196 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -513.463612061 -516.446884735 -516.446884735 Force two-norm initial, final = 6.01123 6.03223e-06 Force max component initial, final = 2.20513 7.07074e-07 Final line search alpha, max atom move = 1 7.07074e-07 Iterations, force evaluations = 190 376 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25457 | 0.25457 | 0.25457 | 0.0 | 96.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0061057 | 0.0061057 | 0.0061057 | 0.0 | 2.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002273 | | | 0.86 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3164 ave 3164 max 3164 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: 27060 ave 27060 max 27060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27060 Ave neighs/atom = 138.061 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) = 4.437 | 4.437 | 4.437 Mbytes Step Temp E_pair E_mol TotEng Press Volume 190 0 -516.44688 0 -516.44688 -8361.8139 3260.2916 1190 0 -516.51931 0 -516.51931 -1388.4113 3231.0188 Loop time of 1.38002 on 1 procs for 1000 steps with 196 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -516.446884735 -516.519305744 -516.519305744 Force two-norm initial, final = 22.51 5.10801e-05 Force max component initial, final = 16.5028 3.57295e-05 Final line search alpha, max atom move = 1 3.57295e-05 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2713 | 1.2713 | 1.2713 | 0.0 | 92.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.028864 | 0.028864 | 0.028864 | 0.0 | 2.09 Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07987 | | | 5.79 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3124 ave 3124 max 3124 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: 27224 ave 27224 max 27224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27224 Ave neighs/atom = 138.898 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 = 3 22 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) = 4.574 | 4.574 | 4.574 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -516.51931 0 -516.51931 -1388.4113 Loop time of 9.53674e-07 on 1 procs for 0 steps with 196 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: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3129 ave 3129 max 3129 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: 27240 ave 27240 max 27240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27240 Ave neighs/atom = 138.98 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) = 4.574 | 4.574 | 4.574 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 -516.51931 -516.51931 8.9568763 90.006328 4.0078353 -1388.4113 -1388.4113 -0.017632767 -4165.2211 0.0047413193 2.6745474 170.34635 Loop time of 1.90735e-06 on 1 procs for 0 steps with 196 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 | | 1.907e-06 | | |100.00 Nlocal: 196 ave 196 max 196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3129 ave 3129 max 3129 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13620 ave 13620 max 13620 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27240 ave 27240 max 27240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27240 Ave neighs/atom = 138.98 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_053.1301/numatoms.out 196 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -516.519305743642-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -516.519305743642-196*${isolated_atom_energy} variable adjusted_pe_metal equal -516.519305743642-196*-0.0307342631051472 print "${adjusted_pe_metal} eV" file output/dump_053.1301/energy.out -510.495390175033 eV print "${mindist_metal} Angstroms" file output/dump_053.1301/mindistance.out 2.67454736672456 Angstroms write_dump all cfg output/dump_053.1301/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_053.1301/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:01