LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 4.032988503575325*${_u_distance} variable lattice_constant_converted equal 4.032988503575325*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 30.71432538178729*${_u_distance} variable xmax_converted equal 30.71432538178729*1 variable ymin_converted equal -61.432683752078155*${_u_distance} variable ymin_converted equal -61.432683752078155*1 variable ymax_converted equal 61.432683752078155*${_u_distance} variable ymax_converted equal 61.432683752078155*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032988503575325*${_u_distance} variable zmax_converted equal 4.032988503575325*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03298850357533 Lattice spacing in x,y,z = 4.03299 4.03299 4.03299 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 30.7143253817873 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.7143253817873 -61.4326837520782 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 30.7143253817873 -61.4326837520782 61.4326837520782 ${zmin_converted} ${zmax_converted} units box region whole block 0 30.7143253817873 -61.4326837520782 61.4326837520782 0 ${zmax_converted} units box region whole block 0 30.7143253817873 -61.4326837520782 61.4326837520782 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -61.4327 0) to (30.7143 61.4327 4.03299) 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 61.4326837520782 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -3 0 orient y 3 7 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 7 -3 0 orient y 3 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.29557 5.29557 4.03299 create_atoms 1 region upper Created 465 atoms create_atoms CPU = 0.000200033 secs group upper type 1 465 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.4270978976387587 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.4326837520782 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 3 0 orient y -3 7 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 7 3 0 orient y -3 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.29557 5.29557 4.03299 create_atoms 2 region lower Created 465 atoms create_atoms CPU = 9.20296e-05 secs group lower type 2 465 atoms in group lower displace_atoms lower move -3.4270978976387587 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Al__MO_140175748626_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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*4.03298850357533 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01649425178767 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 18 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 15 atoms, new total = 915 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2636.7992 0 -2636.7992 -378.19874 518 0 -2657.1541 0 -2657.1541 -7211.3056 Loop time of 12.5089 on 1 procs for 518 steps with 915 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2636.79922334 -2657.15411641 -2657.15411641 Force two-norm initial, final = 14.8262 6.27348e-07 Force max component initial, final = 3.89698 1.74638e-07 Final line search alpha, max atom move = 1 1.74638e-07 Iterations, force evaluations = 518 1015 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.384 | 12.384 | 12.384 | 0.0 | 99.01 Neigh | 0.027543 | 0.027543 | 0.027543 | 0.0 | 0.22 Comm | 0.07585 | 0.07585 | 0.07585 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02105 | | | 0.17 Nlocal: 915 ave 915 max 915 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16069 ave 16069 max 16069 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: 603208 ave 603208 max 603208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603208 Ave neighs/atom = 659.244 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) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press Volume 518 0 -2657.1541 0 -2657.1541 -7211.3056 15219.397 1518 0 -2657.3761 0 -2657.3761 -1880.3673 15108.122 Loop time of 25.7664 on 1 procs for 1000 steps with 915 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 = -2657.15411641 -2657.37608441 -2657.37609024 Force two-norm initial, final = 81.0244 0.213547 Force max component initial, final = 63.4737 0.205381 Final line search alpha, max atom move = 0.0692553 0.0142237 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.251 | 25.251 | 25.251 | 0.0 | 98.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.14454 | 0.14454 | 0.14454 | 0.0 | 0.56 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3711 | | | 1.44 Nlocal: 915 ave 915 max 915 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16045 ave 16045 max 16045 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: 600570 ave 600570 max 600570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 600570 Ave neighs/atom = 656.361 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:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 10.46 | 10.46 | 10.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2657.3761 0 -2657.3761 -1880.3673 Loop time of 9.53674e-07 on 1 procs for 0 steps with 915 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: 915 ave 915 max 915 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16109 ave 16109 max 16109 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: 603186 ave 603186 max 603186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603186 Ave neighs/atom = 659.22 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:52) Per MPI rank memory allocation (min/avg/max) = 10.46 | 10.46 | 10.46 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 -2657.3761 -2657.3761 30.518805 122.86537 4.0291505 -1880.3673 -1880.3673 0.38521145 -5619.7278 -21.759409 2.5141612 490.48434 Loop time of 9.53674e-07 on 1 procs for 0 steps with 915 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: 915 ave 915 max 915 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16109 ave 16109 max 16109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 301593 ave 301593 max 301593 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 603186 ave 603186 max 603186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603186 Ave neighs/atom = 659.22 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_046.3972/numatoms.out 915 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2657.37609023516-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2657.37609023516-915*${isolated_atom_energy} variable adjusted_pe_metal equal -2657.37609023516-915*0 print "${adjusted_pe_metal} eV" file output/dump_046.3972/energy.out -2657.37609023516 eV print "${mindist_metal} Angstroms" file output/dump_046.3972/mindistance.out 2.51416124001574 Angstroms write_dump all cfg output/dump_046.3972/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_046.3972/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:38