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 3.987558534741402*${_u_distance} variable lattice_constant_converted equal 3.987558534741402*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 74.17287631961021*${_u_distance} variable xmax_converted equal 74.17287631961021*1 variable ymin_converted equal -74.17686387814496*${_u_distance} variable ymin_converted equal -74.17686387814496*1 variable ymax_converted equal 74.17686387814496*${_u_distance} variable ymax_converted equal 74.17686387814496*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.987558534741402*${_u_distance} variable zmax_converted equal 3.987558534741402*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.9875585347414 Lattice spacing in x,y,z = 3.98756 3.98756 3.98756 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 74.1728763196102 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 74.1728763196102 -74.176863878145 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 74.1728763196102 -74.176863878145 74.176863878145 ${zmin_converted} ${zmax_converted} units box region whole block 0 74.1728763196102 -74.176863878145 74.176863878145 0 ${zmax_converted} units box region whole block 0 74.1728763196102 -74.176863878145 74.176863878145 0 3.9875585347414 units box create_box 2 whole Created orthogonal box = (0 -74.1769 0) to (74.1729 74.1769 3.98756) 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 74.176863878145 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -11 0 orient y 11 15 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 15 -11 0 orient y 11 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57368 5.57368 3.98756 create_atoms 1 region upper Created 1386 atoms create_atoms CPU = 0.000371933 secs group upper type 1 1386 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.370483856982224 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -74.176863878145 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 11 0 orient y -11 15 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 15 11 0 orient y -11 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57368 5.57368 3.98756 create_atoms 2 region lower Created 1386 atoms create_atoms CPU = 0.000236988 secs group lower type 2 1386 atoms in group lower displace_atoms lower move -8.370483856982224 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_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*3.9875585347414 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.9937792673707 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 ghost atom cutoff = 8 binsize = 4, 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 2738 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 ghost atom cutoff = 8 binsize = 4, bins = 19 38 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.08 | 10.08 | 10.08 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9222.8741 0 -9222.8741 -509.4631 413 0 -9256.5234 0 -9256.5234 -7715.2486 Loop time of 5.78102 on 1 procs for 413 steps with 2738 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9222.87414617 -9256.5234045 -9256.5234045 Force two-norm initial, final = 24.0696 6.06538e-06 Force max component initial, final = 4.64194 6.78886e-07 Final line search alpha, max atom move = 1 6.78886e-07 Iterations, force evaluations = 413 804 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6416 | 5.6416 | 5.6416 | 0.0 | 97.59 Neigh | 0.02961 | 0.02961 | 0.02961 | 0.0 | 0.51 Comm | 0.066501 | 0.066501 | 0.066501 | 0.0 | 1.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04328 | | | 0.75 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15697 ave 15697 max 15697 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: 376928 ave 376928 max 376928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376928 Ave neighs/atom = 137.665 Neighbor list builds = 3 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) = 10.08 | 10.08 | 10.08 Mbytes Step Temp E_pair E_mol TotEng Press Volume 413 0 -9256.5234 0 -9256.5234 -7715.2486 43878.387 1413 0 -9257.0729 0 -9257.0729 -1962.0765 43603.077 Loop time of 16.1348 on 1 procs for 1000 steps with 2738 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -9256.5234045 -9257.07293657 -9257.07293662 Force two-norm initial, final = 240.188 0.0348581 Force max component initial, final = 177.007 0.0326065 Final line search alpha, max atom move = 0.0878725 0.00286522 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.378 | 15.378 | 15.378 | 0.0 | 95.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.16234 | 0.16234 | 0.16234 | 0.0 | 1.01 Output | 2.2173e-05 | 2.2173e-05 | 2.2173e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.594 | | | 3.68 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15712 ave 15712 max 15712 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: 376408 ave 376408 max 376408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376408 Ave neighs/atom = 137.476 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 -1.81000000000002 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 ghost atom cutoff = 8 binsize = 4, bins = 19 38 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 9.589 | 9.589 | 9.589 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9257.0729 0 -9257.0729 -1962.0765 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2738 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: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15717 ave 15717 max 15717 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: 376760 ave 376760 max 376760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376760 Ave neighs/atom = 137.604 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) = 9.589 | 9.589 | 9.589 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 -9257.0729 -9257.0729 74.082215 148.35373 3.9673884 -1962.0765 -1962.0765 0.064209977 -5887.4859 1.1920529 2.532344 750.43492 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2738 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: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15717 ave 15717 max 15717 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 188380 ave 188380 max 188380 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 376760 ave 376760 max 376760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376760 Ave neighs/atom = 137.604 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_072.5077/numatoms.out 2738 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -9257.07293661512-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -9257.07293661512-2738*${isolated_atom_energy} variable adjusted_pe_metal equal -9257.07293661512-2738*-1.81000000000002 print "${adjusted_pe_metal} eV" file output/dump_072.5077/energy.out -4301.29293661507 eV print "${mindist_metal} Angstroms" file output/dump_072.5077/mindistance.out 2.53234403822442 Angstroms write_dump all cfg output/dump_072.5077/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_072.5077/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:22