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 4.050010219216347*${_u_distance} variable lattice_constant_converted equal 4.050010219216347*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 41.69740728426919*${_u_distance} variable xmax_converted equal 41.69740728426919*1 variable ymin_converted equal -41.70145729448841*${_u_distance} variable ymin_converted equal -41.70145729448841*1 variable ymax_converted equal 41.70145729448841*${_u_distance} variable ymax_converted equal 41.70145729448841*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050010219216347*${_u_distance} variable zmax_converted equal 4.050010219216347*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05001021921635 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 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 41.6974072842692 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 41.6974072842692 -41.7014572944884 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 41.6974072842692 -41.7014572944884 41.7014572944884 ${zmin_converted} ${zmax_converted} units box region whole block 0 41.6974072842692 -41.7014572944884 41.7014572944884 0 ${zmax_converted} units box region whole block 0 41.6974072842692 -41.7014572944884 41.7014572944884 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -41.7015 0) to (41.6974 41.7015 4.05001) 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 41.7014572944884 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -5 0 orient y 5 9 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 9 -5 0 orient y 5 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.5072 5.5072 4.05001 create_atoms 1 region upper Created 425 atoms create_atoms CPU = 0.000187159 secs group upper type 1 425 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.63303356344415 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -41.7014572944884 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 5 0 orient y -5 9 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 9 5 0 orient y -5 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.5072 5.5072 4.05001 create_atoms 2 region lower Created 425 atoms create_atoms CPU = 9.89437e-05 secs group lower type 2 425 atoms in group lower displace_atoms lower move -4.63303356344415 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_005 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*4.05001021921635 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500510960818 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 11 22 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 834 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 11 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.937 | 4.937 | 4.937 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2796.5629 0 -2796.5629 3097.1639 266 0 -2814.8216 0 -2814.8216 -6982.6511 Loop time of 0.877906 on 1 procs for 266 steps with 834 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2796.56287283 -2814.82161437 -2814.82161437 Force two-norm initial, final = 27.138 1.59585e-05 Force max component initial, final = 7.40824 5.90037e-06 Final line search alpha, max atom move = 1 5.90037e-06 Iterations, force evaluations = 266 510 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84896 | 0.84896 | 0.84896 | 0.0 | 96.70 Neigh | 0.005918 | 0.005918 | 0.005918 | 0.0 | 0.67 Comm | 0.014676 | 0.014676 | 0.014676 | 0.0 | 1.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008355 | | | 0.95 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5866 ave 5866 max 5866 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: 86342 ave 86342 max 86342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86342 Ave neighs/atom = 103.528 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) = 4.937 | 4.937 | 4.937 Mbytes Step Temp E_pair E_mol TotEng Press Volume 266 0 -2814.8216 0 -2814.8216 -6982.6511 14084.661 1266 0 -2815.0232 0 -2815.0232 -1418.1037 13979.884 Loop time of 4.10629 on 1 procs for 1000 steps with 834 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2814.82161437 -2815.02316856 -2815.02317177 Force two-norm initial, final = 76.8123 0.117941 Force max component initial, final = 56.9411 0.104552 Final line search alpha, max atom move = 0.0267 0.00279154 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8451 | 3.8451 | 3.8451 | 0.0 | 93.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.059131 | 0.059131 | 0.059131 | 0.0 | 1.44 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.202 | | | 4.92 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5881 ave 5881 max 5881 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: 85920 ave 85920 max 85920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85920 Ave neighs/atom = 103.022 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 11 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.694 | 4.694 | 4.694 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2815.0232 0 -2815.0232 -1418.1037 Loop time of 9.53674e-07 on 1 procs for 0 steps with 834 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: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5871 ave 5871 max 5871 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: 94560 ave 94560 max 94560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94560 Ave neighs/atom = 113.381 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) = 4.694 | 4.694 | 4.694 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 -2815.0232 -2815.0232 41.525591 83.402915 4.0365144 -1418.1037 -1418.1037 -2.3482907 -4240.0206 -11.942363 2.5573452 645.23857 Loop time of 1.19209e-06 on 1 procs for 0 steps with 834 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: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5871 ave 5871 max 5871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47280 ave 47280 max 47280 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94560 ave 94560 max 94560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94560 Ave neighs/atom = 113.381 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_058.1092/numatoms.out 834 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2815.02317176842-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2815.02317176842-834*${isolated_atom_energy} variable adjusted_pe_metal equal -2815.02317176842-834*0 print "${adjusted_pe_metal} eV" file output/dump_058.1092/energy.out -2815.02317176842 eV print "${mindist_metal} Angstroms" file output/dump_058.1092/mindistance.out 2.55734519209042 Angstroms write_dump all cfg output/dump_058.1092/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_058.1092/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:05