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 29.484519448604086*${_u_distance} variable xmax_converted equal 29.484519448604086*1 variable ymin_converted equal -58.97308890742739*${_u_distance} variable ymin_converted equal -58.97308890742739*1 variable ymax_converted equal 58.97308890742739*${_u_distance} variable ymax_converted equal 58.97308890742739*1 variable zmin_converted equal 0.0*${_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 29.4845194486041 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 29.4845194486041 -58.9730889074274 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 29.4845194486041 -58.9730889074274 58.9730889074274 ${zmin_converted} ${zmax_converted} units box region whole block 0 29.4845194486041 -58.9730889074274 58.9730889074274 0 ${zmax_converted} units box region whole block 0 29.4845194486041 -58.9730889074274 58.9730889074274 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -58.9731 0) to (29.4845 58.9731 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 58.9730889074274 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -2 0 orient y 2 7 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 7 -2 0 orient y 2 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.00681 5.00681 4.05001 create_atoms 1 region upper Created 426 atoms create_atoms CPU = 0.000254869 secs group upper type 1 426 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.276049450176233 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -58.9730889074274 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 2 0 orient y -2 7 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 7 2 0 orient y -2 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.00681 5.00681 4.05001 create_atoms 2 region lower Created 426 atoms create_atoms CPU = 0.000115156 secs group lower type 2 426 atoms in group lower displace_atoms lower move -3.276049450176233 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 8 32 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 18 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 = 8 32 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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2808.133 0 -2808.133 2.0360928 230 0 -2817.2728 0 -2817.2728 -7530.055 Loop time of 0.939022 on 1 procs for 230 steps with 834 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2808.13303101 -2817.27281464 -2817.27281464 Force two-norm initial, final = 15.5802 7.00376e-06 Force max component initial, final = 5.40257 1.11739e-06 Final line search alpha, max atom move = 1 1.11739e-06 Iterations, force evaluations = 230 447 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91235 | 0.91235 | 0.91235 | 0.0 | 97.16 Neigh | 0.002666 | 0.002666 | 0.002666 | 0.0 | 0.28 Comm | 0.015455 | 0.015455 | 0.015455 | 0.0 | 1.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008552 | | | 0.91 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6276 ave 6276 max 6276 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: 97288 ave 97288 max 97288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97288 Ave neighs/atom = 116.652 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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press Volume 230 0 -2817.2728 0 -2817.2728 -7530.055 14084.26 1230 0 -2817.5099 0 -2817.5099 -1460.4157 13968.803 Loop time of 4.28535 on 1 procs for 1000 steps with 834 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 = -2817.27281464 -2817.50985462 -2817.50985684 Force two-norm initial, final = 81.701 0.121678 Force max component initial, final = 59.9822 0.100694 Final line search alpha, max atom move = 0.0721105 0.0072611 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9957 | 3.9957 | 3.9957 | 0.0 | 93.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.064852 | 0.064852 | 0.064852 | 0.0 | 1.51 Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2248 | | | 5.25 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6281 ave 6281 max 6281 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: 84236 ave 84236 max 84236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84236 Ave neighs/atom = 101.002 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 = 8 32 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) = 4.711 | 4.711 | 4.711 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2817.5099 0 -2817.5099 -1460.4157 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: 6301 ave 6301 max 6301 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: 93484 ave 93484 max 93484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93484 Ave neighs/atom = 112.091 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) = 4.711 | 4.711 | 4.711 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 -2817.5099 -2817.5099 29.334067 117.94618 4.0374116 -1460.4157 -1460.4157 -11.490347 -4365.7615 -3.9950824 2.6211979 483.57956 Loop time of 1.90735e-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 | | 1.907e-06 | | |100.00 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6301 ave 6301 max 6301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46742 ave 46742 max 46742 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 93484 ave 93484 max 93484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93484 Ave neighs/atom = 112.091 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_031.8908/numatoms.out 834 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2817.50985683947-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2817.50985683947-834*${isolated_atom_energy} variable adjusted_pe_metal equal -2817.50985683947-834*0 print "${adjusted_pe_metal} eV" file output/dump_031.8908/energy.out -2817.50985683947 eV print "${mindist_metal} Angstroms" file output/dump_031.8908/mindistance.out 2.62119788191045 Angstroms write_dump all cfg output/dump_031.8908/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_031.8908/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:05