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 4.210700303316116*${_u_distance} variable lattice_constant_converted equal 4.210700303316116*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 83.58001456970736*${_u_distance} variable xmax_converted equal 83.58001456970736*1 variable ymin_converted equal -83.58422527001068*${_u_distance} variable ymin_converted equal -83.58422527001068*1 variable ymax_converted equal 83.58422527001068*${_u_distance} variable ymax_converted equal 83.58422527001068*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.210700303316116*${_u_distance} variable zmax_converted equal 4.210700303316116*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.21070030331612 Lattice spacing in x,y,z = 4.2107 4.2107 4.2107 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 83.5800145697074 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 83.5800145697074 -83.5842252700107 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 83.5800145697074 -83.5842252700107 83.5842252700107 ${zmin_converted} ${zmax_converted} units box region whole block 0 83.5800145697074 -83.5842252700107 83.5842252700107 0 ${zmax_converted} units box region whole block 0 83.5800145697074 -83.5842252700107 83.5842252700107 0 4.21070030331612 units box create_box 2 whole Created orthogonal box = (0 -83.5842 0) to (83.58 83.5842 4.2107) 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 83.5842252700107 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 lattice fcc 4.21070030331612 orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.9397 5.9397 4.2107 create_atoms 1 region upper Created 1578 atoms create_atoms CPU = 0.000365973 secs group upper type 1 1578 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.932244958575643 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -83.5842252700107 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 lattice fcc 4.21070030331612 orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.9397 5.9397 4.2107 create_atoms 2 region lower Created 1578 atoms create_atoms CPU = 0.000275135 secs group lower type 2 1578 atoms in group lower displace_atoms lower move -8.932244958575643 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_SchopfBrommerFrigan_2012_AlMnPd__MO_878712978062_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*4.21070030331612 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.10535015165806 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 ghost atom cutoff = 9 binsize = 4.5, bins = 19 38 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 3120 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 ghost atom cutoff = 9 binsize = 4.5, bins = 19 38 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.93 | 10.93 | 10.93 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11602.49 0 -11602.49 -376.13511 437 0 -11620.228 0 -11620.228 -2772.2619 Loop time of 17.2805 on 1 procs for 437 steps with 3120 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 = -11602.4901677 -11620.2283501 -11620.2283501 Force two-norm initial, final = 17.8392 2.61883e-05 Force max component initial, final = 5.09159 3.51947e-06 Final line search alpha, max atom move = 1 3.51947e-06 Iterations, force evaluations = 437 858 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.095 | 17.095 | 17.095 | 0.0 | 98.93 Neigh | 0.037874 | 0.037874 | 0.037874 | 0.0 | 0.22 Comm | 0.091149 | 0.091149 | 0.091149 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05616 | | | 0.32 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18030 ave 18030 max 18030 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: 534856 ave 534856 max 534856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 534856 Ave neighs/atom = 171.428 Neighbor list builds = 3 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) = 10.93 | 10.93 | 10.93 Mbytes Step Temp E_pair E_mol TotEng Press Volume 437 0 -11620.228 0 -11620.228 -2772.2619 58831.658 1437 0 -11620.466 0 -11620.466 -635.05284 58503.927 Loop time of 38.2903 on 1 procs for 1000 steps with 3120 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 = -11620.2283501 -11620.4659819 -11620.4659819 Force two-norm initial, final = 120.269 0.0103421 Force max component initial, final = 86.0985 0.00962823 Final line search alpha, max atom move = 0.0292333 0.000281465 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 37.452 | 37.452 | 37.452 | 0.0 | 97.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.18278 | 0.18278 | 0.18278 | 0.0 | 0.48 Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.6555 | | | 1.71 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18006 ave 18006 max 18006 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: 534796 ave 534796 max 534796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 534796 Ave neighs/atom = 171.409 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 ghost atom cutoff = 9 binsize = 4.5, bins = 19 38 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 10.44 | 10.44 | 10.44 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11620.466 0 -11620.466 -635.05284 Loop time of 1.19209e-06 on 1 procs for 0 steps with 3120 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 | | 1.192e-06 | | |100.00 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18065 ave 18065 max 18065 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: 536860 ave 536860 max 536860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536860 Ave neighs/atom = 172.071 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) = 10.44 | 10.44 | 10.44 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 -11620.466 -11620.466 83.338328 167.16845 4.1993872 -635.05284 -635.05284 -0.2629142 -1904.8095 -0.086061603 2.7325253 1026.7971 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3120 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 | | 1.907e-06 | | |100.00 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18065 ave 18065 max 18065 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 268430 ave 268430 max 268430 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 536860 ave 536860 max 536860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536860 Ave neighs/atom = 172.071 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_081.8288/numatoms.out 3120 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11620.46598193-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11620.46598193-3120*${isolated_atom_energy} variable adjusted_pe_metal equal -11620.46598193-3120*0 print "${adjusted_pe_metal} eV" file output/dump_081.8288/energy.out -11620.46598193 eV print "${mindist_metal} Angstroms" file output/dump_081.8288/mindistance.out 2.73252532186846 Angstroms write_dump all cfg output/dump_081.8288/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_081.8288/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:55