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 3.9946166351437573*${_u_distance} variable lattice_constant_converted equal 3.9946166351437573*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 34.13001949177598*${_u_distance} variable xmax_converted equal 34.13001949177598*1 variable ymin_converted equal -68.2640336001871*${_u_distance} variable ymin_converted equal -68.2640336001871*1 variable ymax_converted equal 68.2640336001871*${_u_distance} variable ymax_converted equal 68.2640336001871*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.9946166351437573*${_u_distance} variable zmax_converted equal 3.9946166351437573*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.99461663514376 Lattice spacing in x,y,z = 3.99462 3.99462 3.99462 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 34.130019491776 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.130019491776 -68.2640336001871 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 34.130019491776 -68.2640336001871 68.2640336001871 ${zmin_converted} ${zmax_converted} units box region whole block 0 34.130019491776 -68.2640336001871 68.2640336001871 0 ${zmax_converted} units box region whole block 0 34.130019491776 -68.2640336001871 68.2640336001871 0 3.99461663514376 units box create_box 2 whole Created orthogonal box = (0 -68.264 0) to (34.13 68.264 3.99462) 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 68.2640336001871 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 -3 0 orient y 3 8 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 8 -3 0 orient y 3 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.14288 5.14288 3.99462 create_atoms 1 region upper Created 586 atoms create_atoms CPU = 0.000291109 secs group upper type 1 586 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.844801685392889 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -68.2640336001871 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 3 0 orient y -3 8 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 8 3 0 orient y -3 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.14288 5.14288 3.99462 create_atoms 2 region lower Created 586 atoms create_atoms CPU = 0.000159025 secs group lower type 2 586 atoms in group lower displace_atoms lower move -3.844801685392889 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001 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*3.99461663514376 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.99730831757188 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 9 36 2 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1154 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.044 | 5.044 | 5.044 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3774.5467 0 -3774.5467 -154.656 144 0 -3781.2505 0 -3781.2505 -3048.3048 Loop time of 2.47291 on 1 procs for 144 steps with 1154 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -3774.54671014 -3781.25049219 -3781.25049219 Force two-norm initial, final = 7.20611 0.00697747 Force max component initial, final = 2.00369 0.000968296 Final line search alpha, max atom move = 0.000244141 2.364e-07 Iterations, force evaluations = 144 302 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4461 | 2.4461 | 2.4461 | 0.0 | 98.92 Neigh | 0.0039752 | 0.0039752 | 0.0039752 | 0.0 | 0.16 Comm | 0.014547 | 0.014547 | 0.014547 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008282 | | | 0.33 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8076 ave 8076 max 8076 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: 151816 ave 151816 max 151816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151816 Ave neighs/atom = 131.556 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) = 5.044 | 5.044 | 5.044 Mbytes Step Temp E_pair E_mol TotEng Press Volume 144 0 -3781.2505 0 -3781.2505 -3048.3048 18613.737 149 0 -3781.3406 0 -3781.3406 -828.53886 18508.212 Loop time of 0.306969 on 1 procs for 5 steps with 1154 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -3781.25049219 -3781.34058364 -3781.34058364 Force two-norm initial, final = 42.8453 0.110326 Force max component initial, final = 32.8852 0.0629633 Final line search alpha, max atom move = 9.69377e-07 6.10352e-08 Iterations, force evaluations = 5 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30068 | 0.30068 | 0.30068 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014672 | 0.0014672 | 0.0014672 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00482 | | | 1.57 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7790 ave 7790 max 7790 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: 151976 ave 151976 max 151976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151976 Ave neighs/atom = 131.695 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 -6.30324000329931e-20 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 5.18 | 5.18 | 5.18 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3781.3406 0 -3781.3406 -828.53886 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1154 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: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7823 ave 7823 max 7823 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: 152132 ave 152132 max 152132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152132 Ave neighs/atom = 131.83 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) = 5.18 | 5.18 | 5.18 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 -3781.3406 -3781.3406 34.023807 136.52807 3.9843695 -828.53886 -828.53886 -5.433501 -2485.4271 5.2439868 2.5118467 562.81678 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1154 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: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7823 ave 7823 max 7823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76066 ave 76066 max 76066 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 152132 ave 152132 max 152132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152132 Ave neighs/atom = 131.83 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_041.1121/numatoms.out 1154 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3781.34058364161-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3781.34058364161-1154*${isolated_atom_energy} variable adjusted_pe_metal equal -3781.34058364161-1154*-6.30324000329931e-20 print "${adjusted_pe_metal} eV" file output/dump_041.1121/energy.out -3781.34058364161 eV print "${mindist_metal} Angstroms" file output/dump_041.1121/mindistance.out 2.51184673901507 Angstroms write_dump all cfg output/dump_041.1121/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_041.1121/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:02