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 4.061213478446007*${_u_distance} variable lattice_constant_converted equal 4.061213478446007*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 54.183345922128595*${_u_distance} variable xmax_converted equal 54.183345922128595*1 variable ymin_converted equal -54.18740713560704*${_u_distance} variable ymin_converted equal -54.18740713560704*1 variable ymax_converted equal 54.18740713560704*${_u_distance} variable ymax_converted equal 54.18740713560704*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.061213478446007*${_u_distance} variable zmax_converted equal 4.061213478446007*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.06121347844601 Lattice spacing in x,y,z = 4.06121 4.06121 4.06121 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 54.1833459221286 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 54.1833459221286 -54.187407135607 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 54.1833459221286 -54.187407135607 54.187407135607 ${zmin_converted} ${zmax_converted} units box region whole block 0 54.1833459221286 -54.187407135607 54.187407135607 0 ${zmax_converted} units box region whole block 0 54.1833459221286 -54.187407135607 54.187407135607 0 4.06121347844601 units box create_box 2 whole Created orthogonal box = (0 -54.1874 0) to (54.1833 54.1874 4.06121) 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 54.187407135607 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -3 0 orient y 3 13 0 orient z 0 0 1 lattice fcc 4.06121347844601 orient x 13 -3 0 orient y 3 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.87041 4.87041 4.06121 create_atoms 1 region upper Created 714 atoms create_atoms CPU = 0.000218868 secs group upper type 1 714 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.003748828856851 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -54.187407135607 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 3 0 orient y -3 13 0 orient z 0 0 1 lattice fcc 4.06121347844601 orient x 13 3 0 orient y -3 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.87041 4.87041 4.06121 create_atoms 2 region lower Created 714 atoms create_atoms CPU = 0.000108957 secs group lower type 2 714 atoms in group lower displace_atoms lower move -6.003748828856851 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959LowCutoff_Al__MO_411898953661_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*4.06121347844601 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03060673922301 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 12 23 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1408 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 12 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.926 | 5.926 | 5.926 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3738.2504 0 -3738.2504 1933.0805 322 0 -3774.5274 0 -3774.5274 -3853.9717 Loop time of 4.91724 on 1 procs for 322 steps with 1408 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3738.2503508 -3774.52743628 -3774.52743628 Force two-norm initial, final = 29.165 5.06932e-06 Force max component initial, final = 5.3614 4.95668e-07 Final line search alpha, max atom move = 1 4.95668e-07 Iterations, force evaluations = 322 634 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8385 | 4.8385 | 4.8385 | 0.0 | 98.40 Neigh | 0.013527 | 0.013527 | 0.013527 | 0.0 | 0.28 Comm | 0.045199 | 0.045199 | 0.045199 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02004 | | | 0.41 Nlocal: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12146 ave 12146 max 12146 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: 314216 ave 314216 max 314216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314216 Ave neighs/atom = 223.165 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) = 5.926 | 5.926 | 5.926 Mbytes Step Temp E_pair E_mol TotEng Press Volume 322 0 -3774.5274 0 -3774.5274 -3853.9717 23847.892 1322 0 -3774.6725 0 -3774.6725 -673.10563 23742.824 Loop time of 15.2807 on 1 procs for 1000 steps with 1408 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 = -3774.52743628 -3774.67254275 -3774.6725442 Force two-norm initial, final = 74.8216 0.0983575 Force max component initial, final = 63.5754 0.0609449 Final line search alpha, max atom move = 0.0282598 0.00172229 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.764 | 14.764 | 14.764 | 0.0 | 96.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12557 | 0.12557 | 0.12557 | 0.0 | 0.82 Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3916 | | | 2.56 Nlocal: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12158 ave 12158 max 12158 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: 314464 ave 314464 max 314464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314464 Ave neighs/atom = 223.341 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 11 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 6.064 | 6.064 | 6.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3774.6725 0 -3774.6725 -673.10563 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1408 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: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12176 ave 12176 max 12176 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: 314912 ave 314912 max 314912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314912 Ave neighs/atom = 223.659 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) = 6.064 | 6.064 | 6.064 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 -3774.6725 -3774.6725 53.887326 108.37481 4.0655318 -673.10563 -673.10563 -4.0901198 -2013.4629 -1.7638712 2.5745967 818.40895 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1408 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 | | 2.146e-06 | | |100.00 Nlocal: 1408 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12176 ave 12176 max 12176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 157456 ave 157456 max 157456 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 314912 ave 314912 max 314912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314912 Ave neighs/atom = 223.659 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_025.9892/numatoms.out 1408 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3774.6725442005-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3774.6725442005-1408*${isolated_atom_energy} variable adjusted_pe_metal equal -3774.6725442005-1408*0 print "${adjusted_pe_metal} eV" file output/dump_025.9892/energy.out -3774.6725442005 eV print "${mindist_metal} Angstroms" file output/dump_025.9892/mindistance.out 2.57459673255913 Angstroms write_dump all cfg output/dump_025.9892/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_025.9892/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:20