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 4.05000014603138*${_u_distance} variable lattice_constant_converted equal 4.05000014603138*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 68.85000248253345*${_u_distance} variable xmax_converted equal 68.85000248253345*1 variable ymin_converted equal -68.85405248267949*${_u_distance} variable ymin_converted equal -68.85405248267949*1 variable ymax_converted equal 68.85405248267949*${_u_distance} variable ymax_converted equal 68.85405248267949*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.05000014603138*${_u_distance} variable zmax_converted equal 4.05000014603138*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000014603138 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 68.8500024825335 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8500024825335 -68.8540524826795 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8500024825335 -68.8540524826795 68.8540524826795 ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8500024825335 -68.8540524826795 68.8540524826795 0 ${zmax_converted} units box region whole block 0 68.8500024825335 -68.8540524826795 68.8540524826795 0 4.05000014603138 units box create_box 2 whole Created orthogonal box = (0 -68.8541 0) to (68.85 68.8541 4.05) 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 68.8540524826795 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -8 0 orient y 8 15 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 15 -8 0 orient y 8 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.47941 5.47941 4.05 create_atoms 1 region upper Created 1158 atoms create_atoms CPU = 0.00040102 secs group upper type 1 1158 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.65 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -68.8540524826795 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 8 0 orient y -8 15 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 15 8 0 orient y -8 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.47941 5.47941 4.05 create_atoms 2 region lower Created 1158 atoms create_atoms CPU = 0.000283957 secs group lower type 2 1158 atoms in group lower displace_atoms lower move -7.65 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_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*4.05000014603138 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500007301569 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 17 33 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 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 2282 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 17 33 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.083 | 6.083 | 6.083 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7623.5024 0 -7623.5024 -2098.1483 300 0 -7646.4333 0 -7646.4333 -6882.332 Loop time of 5.1578 on 1 procs for 300 steps with 2282 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7623.50238767 -7646.43332802 -7646.43332802 Force two-norm initial, final = 14.6601 1.40687e-05 Force max component initial, final = 1.95955 2.69947e-06 Final line search alpha, max atom move = 1 2.69947e-06 Iterations, force evaluations = 300 586 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.066 | 5.066 | 5.066 | 0.0 | 98.22 Neigh | 0.01761 | 0.01761 | 0.01761 | 0.0 | 0.34 Comm | 0.045117 | 0.045117 | 0.045117 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02908 | | | 0.56 Nlocal: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13673 ave 13673 max 13673 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: 320812 ave 320812 max 320812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320812 Ave neighs/atom = 140.584 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) = 6.084 | 6.084 | 6.084 Mbytes Step Temp E_pair E_mol TotEng Press Volume 300 0 -7646.4333 0 -7646.4333 -6882.332 38398.875 1300 0 -7646.8956 0 -7646.8956 -1744.666 38146.512 Loop time of 17.901 on 1 procs for 1000 steps with 2282 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 = -7646.43332802 -7646.89564018 -7646.89564024 Force two-norm initial, final = 195.554 0.0468076 Force max component initial, final = 146.882 0.0458176 Final line search alpha, max atom move = 0.076769 0.00351737 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.239 | 17.239 | 17.239 | 0.0 | 96.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.14288 | 0.14288 | 0.14288 | 0.0 | 0.80 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5193 | | | 2.90 Nlocal: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13683 ave 13683 max 13683 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: 320464 ave 320464 max 320464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320464 Ave neighs/atom = 140.431 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 17 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 6.222 | 6.222 | 6.222 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7646.8956 0 -7646.8956 -1744.666 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2282 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: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13688 ave 13688 max 13688 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: 321040 ave 321040 max 321040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321040 Ave neighs/atom = 140.684 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) = 6.222 | 6.222 | 6.222 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 -7646.8956 -7646.8956 68.678164 137.7081 4.0334498 -1744.666 -1744.666 -0.11856844 -5235.7961 1.9165012 2.5824773 1279.1851 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2282 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: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13688 ave 13688 max 13688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160520 ave 160520 max 160520 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 321040 ave 321040 max 321040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321040 Ave neighs/atom = 140.684 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_056.1450/numatoms.out 2282 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7646.89564023575-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7646.89564023575-2282*${isolated_atom_energy} variable adjusted_pe_metal equal -7646.89564023575-2282*0 print "${adjusted_pe_metal} eV" file output/dump_056.1450/energy.out -7646.89564023575 eV print "${mindist_metal} Angstroms" file output/dump_056.1450/mindistance.out 2.5824773424486 Angstroms write_dump all cfg output/dump_056.1450/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_056.1450/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:23