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 5.727565134130592*${_u_distance} variable xmax_converted equal 5.727565134130592*1 variable ymin_converted equal -45.82457107319077*${_u_distance} variable ymin_converted equal -45.82457107319077*1 variable ymax_converted equal 45.82457107319077*${_u_distance} variable ymax_converted equal 45.82457107319077*1 variable zmin_converted equal 0.0*${_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 5.72756513413059 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 5.72756513413059 -45.8245710731908 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 5.72756513413059 -45.8245710731908 45.8245710731908 ${zmin_converted} ${zmax_converted} units box region whole block 0 5.72756513413059 -45.8245710731908 45.8245710731908 0 ${zmax_converted} units box region whole block 0 5.72756513413059 -45.8245710731908 45.8245710731908 0 4.05000014603138 units box create_box 2 whole Created orthogonal box = (0 -45.8246 0) to (5.72757 45.8246 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 45.8245710731908 INF INF units box lattice fcc ${lattice_constant_converted} orient x 1 -1 0 orient y 1 1 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 1 -1 0 orient y 1 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72757 5.72757 4.05 create_atoms 1 region upper Created 66 atoms create_atoms CPU = 0.000181913 secs group upper type 1 66 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 0.6363961030678927 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.8245710731908 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 1 1 0 orient y -1 1 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 1 1 0 orient y -1 1 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72757 5.72757 4.05 create_atoms 2 region lower Created 66 atoms create_atoms CPU = 5.60284e-05 secs group lower type 2 66 atoms in group lower displace_atoms lower move -0.6363961030678927 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 2 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 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 124 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 = 2 22 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) = 4.428 | 4.428 | 4.428 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -412.99625 0 -412.99625 -6346.9232 138 0 -415.8511 0 -415.8511 -24480.572 Loop time of 0.15472 on 1 procs for 138 steps with 124 atoms 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -412.996245125 -415.851096053 -415.851096053 Force two-norm initial, final = 1.62419 3.7694e-07 Force max component initial, final = 0.527858 5.46786e-08 Final line search alpha, max atom move = 1 5.46786e-08 Iterations, force evaluations = 138 268 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14915 | 0.14915 | 0.14915 | 0.0 | 96.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0042388 | 0.0042388 | 0.0042388 | 0.0 | 2.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001336 | | | 0.86 Nlocal: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2756 ave 2756 max 2756 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: 16968 ave 16968 max 16968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16968 Ave neighs/atom = 136.839 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) = 4.429 | 4.429 | 4.429 Mbytes Step Temp E_pair E_mol TotEng Press Volume 138 0 -415.8511 0 -415.8511 -24480.572 2125.9521 278 0 -416.09624 0 -416.09624 -9012.8981 2082.7368 Loop time of 0.169636 on 1 procs for 140 steps with 124 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -415.851096053 -416.096243755 -416.096243755 Force two-norm initial, final = 33.4341 4.67306e-10 Force max component initial, final = 24.6218 1.36384e-10 Final line search alpha, max atom move = 1 1.36384e-10 Iterations, force evaluations = 140 269 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1528 | 0.1528 | 0.1528 | 0.0 | 90.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043373 | 0.0043373 | 0.0043373 | 0.0 | 2.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01249 | | | 7.37 Nlocal: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2836 ave 2836 max 2836 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: 17360 ave 17360 max 17360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17360 Ave neighs/atom = 140 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 = 2 22 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) = 4.567 | 4.567 | 4.567 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -416.09624 0 -416.09624 -9012.8981 Loop time of 9.53674e-07 on 1 procs for 0 steps with 124 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: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2836 ave 2836 max 2836 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: 17856 ave 17856 max 17856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17856 Ave neighs/atom = 144 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) = 4.567 | 4.567 | 4.567 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 -416.09624 -416.09624 5.6799595 91.649142 4.0009281 -9012.8981 -9012.8981 3.0697192e-08 -27038.694 -1.7173499e-09 2.8399798 9.9631098e-19 Loop time of 9.53674e-07 on 1 procs for 0 steps with 124 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: 124 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2836 ave 2836 max 2836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8928 ave 8928 max 8928 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17856 ave 17856 max 17856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17856 Ave neighs/atom = 144 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_090.0000/numatoms.out 124 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -416.096243755494-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -416.096243755494-124*${isolated_atom_energy} variable adjusted_pe_metal equal -416.096243755494-124*0 print "${adjusted_pe_metal} eV" file output/dump_090.0000/energy.out -416.096243755494 eV print "${mindist_metal} Angstroms" file output/dump_090.0000/mindistance.out 2.83997976988505 Angstroms write_dump all cfg output/dump_090.0000/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_090.0000/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:00