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 4.024845376610756*${_u_distance} variable lattice_constant_converted equal 4.024845376610756*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 79.89089960950648*${_u_distance} variable xmax_converted equal 79.89089960950648*1 variable ymin_converted equal -79.89492445488308*${_u_distance} variable ymin_converted equal -79.89492445488308*1 variable ymax_converted equal 79.89492445488308*${_u_distance} variable ymax_converted equal 79.89492445488308*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.024845376610756*${_u_distance} variable zmax_converted equal 4.024845376610756*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.02484537661076 Lattice spacing in x,y,z = 4.02485 4.02485 4.02485 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 79.8908996095065 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 79.8908996095065 -79.8949244548831 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 79.8908996095065 -79.8949244548831 79.8949244548831 ${zmin_converted} ${zmax_converted} units box region whole block 0 79.8908996095065 -79.8949244548831 79.8949244548831 0 ${zmax_converted} units box region whole block 0 79.8908996095065 -79.8949244548831 79.8949244548831 0 4.02484537661076 units box create_box 2 whole Created orthogonal box = (0 -79.8949 0) to (79.8909 79.8949 4.02485) 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 79.8949244548831 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 15 -13 0 orient y 13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67753 5.67753 4.02485 create_atoms 1 region upper Created 1578 atoms create_atoms CPU = 0.000545025 secs group upper type 1 1578 atoms in group upper mass 1 26.981538*${_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 -79.8949244548831 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 lattice fcc 4.02484537661076 orient x 15 13 0 orient y -13 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.67753 5.67753 4.02485 create_atoms 2 region lower Created 1578 atoms create_atoms CPU = 0.000390768 secs group lower type 2 1578 atoms in group lower displace_atoms lower move -8.932244958575643 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_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*4.02484537661076 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01242268830538 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 20 39 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 8.365 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 20 39 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.54 | 10.54 | 10.54 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8214.5247 0 -8214.5247 -1701.8598 364 0 -8243.4071 0 -8243.4071 -6039.6269 Loop time of 7.28255 on 1 procs for 364 steps with 3120 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8214.52473865 -8243.4070952 -8243.4070952 Force two-norm initial, final = 15.9174 1.90938e-05 Force max component initial, final = 2.60981 3.81623e-06 Final line search alpha, max atom move = 1 3.81623e-06 Iterations, force evaluations = 364 718 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1244 | 7.1244 | 7.1244 | 0.0 | 97.83 Neigh | 0.039717 | 0.039717 | 0.039717 | 0.0 | 0.55 Comm | 0.071799 | 0.071799 | 0.071799 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04661 | | | 0.64 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17685 ave 17685 max 17685 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: 437320 ave 437320 max 437320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437320 Ave neighs/atom = 140.167 Neighbor list builds = 4 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) = 10.55 | 10.55 | 10.55 Mbytes Step Temp E_pair E_mol TotEng Press Volume 364 0 -8243.4071 0 -8243.4071 -6039.6269 51380.189 1364 0 -8243.8803 0 -8243.8803 -1593.6283 51088.688 Loop time of 22.0029 on 1 procs for 1000 steps with 3120 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -8243.4070952 -8243.88026759 -8243.88026759 Force two-norm initial, final = 226.748 0.000533925 Force max component initial, final = 175.454 0.000291417 Final line search alpha, max atom move = 0.928316 0.000270527 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.14 | 21.14 | 21.14 | 0.0 | 96.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.18361 | 0.18361 | 0.18361 | 0.0 | 0.83 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.6788 | | | 3.09 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17690 ave 17690 max 17690 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: 437384 ave 437384 max 437384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437384 Ave neighs/atom = 140.187 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 -0.0307342631051472 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 20 39 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 10.06 | 10.06 | 10.06 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8243.8803 0 -8243.8803 -1593.6283 Loop time of 9.53674e-07 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 | | 9.537e-07 | | |100.00 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17690 ave 17690 max 17690 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: 437496 ave 437496 max 437496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437496 Ave neighs/atom = 140.223 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) = 10.06 | 10.06 | 10.06 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 -8243.8803 -8243.8803 79.749455 159.78985 4.0091088 -1593.6283 -1593.6283 0.004087114 -4780.8982 0.009103306 2.5771071 397.16775 Loop time of 9.53674e-07 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 | | 9.537e-07 | | |100.00 Nlocal: 3120 ave 3120 max 3120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17690 ave 17690 max 17690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218748 ave 218748 max 218748 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 437496 ave 437496 max 437496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437496 Ave neighs/atom = 140.223 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -8243.8802675873-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8243.8802675873-3120*${isolated_atom_energy} variable adjusted_pe_metal equal -8243.8802675873-3120*-0.0307342631051472 print "${adjusted_pe_metal} eV" file output/dump_081.8288/energy.out -8147.98936669924 eV print "${mindist_metal} Angstroms" file output/dump_081.8288/mindistance.out 2.57710711913371 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: 0:00:29