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 4.073718130588532*${_u_distance} variable lattice_constant_converted equal 4.073718130588532*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 21.937643511031126*${_u_distance} variable xmax_converted equal 21.937643511031126*1 variable ymin_converted equal -43.879360740192844*${_u_distance} variable ymin_converted equal -43.879360740192844*1 variable ymax_converted equal 43.879360740192844*${_u_distance} variable ymax_converted equal 43.879360740192844*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.073718130588532*${_u_distance} variable zmax_converted equal 4.073718130588532*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.07371813058853 Lattice spacing in x,y,z = 4.07372 4.07372 4.07372 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 21.9376435110311 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 21.9376435110311 -43.8793607401928 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 21.9376435110311 -43.8793607401928 43.8793607401928 ${zmin_converted} ${zmax_converted} units box region whole block 0 21.9376435110311 -43.8793607401928 43.8793607401928 0 ${zmax_converted} units box region whole block 0 21.9376435110311 -43.8793607401928 43.8793607401928 0 4.07371813058853 units box create_box 2 whole Created orthogonal box = (0 -43.8794 0) to (21.9376 43.8794 4.07372) 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 43.8793607401928 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -2 0 orient y 2 5 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 5 -2 0 orient y 2 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.29529 5.29529 4.07372 create_atoms 1 region upper Created 234 atoms create_atoms CPU = 0.000169992 secs group upper type 1 234 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.4233241632105265 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -43.8793607401928 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 2 0 orient y -2 5 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 5 2 0 orient y -2 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.29529 5.29529 4.07372 create_atoms 2 region lower Created 234 atoms create_atoms CPU = 5.10216e-05 secs group lower type 2 234 atoms in group lower displace_atoms lower move -2.4233241632105265 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.07371813058853 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03685906529426 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 5 19 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 458 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1385.8301 0 -1385.8301 5925.305 251 0 -1399.497 0 -1399.497 -1651.522 Loop time of 1.4052 on 1 procs for 251 steps with 458 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1385.83010903 -1399.49699207 -1399.49699207 Force two-norm initial, final = 25.3624 6.55412e-06 Force max component initial, final = 7.04747 7.53983e-07 Final line search alpha, max atom move = 1 7.53983e-07 Iterations, force evaluations = 251 494 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3818 | 1.3818 | 1.3818 | 0.0 | 98.34 Neigh | 0.0016029 | 0.0016029 | 0.0016029 | 0.0 | 0.11 Comm | 0.015266 | 0.015266 | 0.015266 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006508 | | | 0.46 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5150 ave 5150 max 5150 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: 90360 ave 90360 max 90360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90360 Ave neighs/atom = 197.293 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) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press Volume 251 0 -1399.497 0 -1399.497 -1651.522 7842.8018 1251 0 -1399.5116 0 -1399.5116 -163.40835 7818.9306 Loop time of 5.34289 on 1 procs for 1000 steps with 458 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 = -1399.49699207 -1399.51164974 -1399.51164975 Force two-norm initial, final = 12.1422 0.00442288 Force max component initial, final = 10.3037 0.00405278 Final line search alpha, max atom move = 1 0.00405278 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.136 | 5.136 | 5.136 | 0.0 | 96.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.053059 | 0.053059 | 0.053059 | 0.0 | 0.99 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1538 | | | 2.88 Nlocal: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5187 ave 5187 max 5187 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: 90496 ave 90496 max 90496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90496 Ave neighs/atom = 197.59 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 0.143095413925774 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 4.647 | 4.647 | 4.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1399.5116 0 -1399.5116 -163.40835 Loop time of 9.53674e-07 on 1 procs for 0 steps with 458 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: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5191 ave 5191 max 5191 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: 90512 ave 90512 max 90512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90512 Ave neighs/atom = 197.624 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) = 4.647 | 4.647 | 4.647 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 -1399.5116 -1399.5116 21.88307 87.758721 4.0714473 -163.40835 -163.40835 -0.27787177 -489.1172 -0.82999243 2.5657531 362.69065 Loop time of 9.53674e-07 on 1 procs for 0 steps with 458 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: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5191 ave 5191 max 5191 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45256 ave 45256 max 45256 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90512 ave 90512 max 90512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90512 Ave neighs/atom = 197.624 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_043.6028/numatoms.out 458 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1399.51164974732-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1399.51164974732-458*${isolated_atom_energy} variable adjusted_pe_metal equal -1399.51164974732-458*0.143095413925774 print "${adjusted_pe_metal} eV" file output/dump_043.6028/energy.out -1465.04934932532 eV print "${mindist_metal} Angstroms" file output/dump_043.6028/mindistance.out 2.56575308732912 Angstroms write_dump all cfg output/dump_043.6028/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_043.6028/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06