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 4.051526293158533*${_u_distance} variable lattice_constant_converted equal 4.051526293158533*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 68.87594698369506*${_u_distance} variable xmax_converted equal 68.87594698369506*1 variable ymin_converted equal -68.87999850998821*${_u_distance} variable ymin_converted equal -68.87999850998821*1 variable ymax_converted equal 68.87999850998821*${_u_distance} variable ymax_converted equal 68.87999850998821*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.051526293158533*${_u_distance} variable zmax_converted equal 4.051526293158533*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05152629315853 Lattice spacing in x,y,z = 4.05153 4.05153 4.05153 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 68.8759469836951 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8759469836951 -68.8799985099882 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8759469836951 -68.8799985099882 68.8799985099882 ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8759469836951 -68.8799985099882 68.8799985099882 0 ${zmax_converted} units box region whole block 0 68.8759469836951 -68.8799985099882 68.8799985099882 0 4.05152629315853 units box create_box 2 whole Created orthogonal box = (0 -68.88 0) to (68.8759 68.88 4.05153) 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 68.8799985099882 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -8 0 orient y 8 15 0 orient z 0 0 1 lattice fcc 4.05152629315853 orient x 15 -8 0 orient y 8 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.48148 5.48148 4.05153 create_atoms 1 region upper Created 1158 atoms create_atoms CPU = 0.000295877 secs group upper type 1 1158 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.65 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -68.8799985099882 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 8 0 orient y -8 15 0 orient z 0 0 1 lattice fcc 4.05152629315853 orient x 15 8 0 orient y -8 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.48148 5.48148 4.05153 create_atoms 2 region lower Created 1158 atoms create_atoms CPU = 0.000218868 secs group lower type 2 1158 atoms in group lower displace_atoms lower move -7.65 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MishinMehlPapaconstantopoulos_2002_NiAl__MO_109933561507_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*4.05152629315853 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02576314657927 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 18 35 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 7.95414 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 2282 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 18 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.95414 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.058 | 6.058 | 6.058 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7592.7054 0 -7592.7054 5268.9946 307 0 -7638.7853 0 -7638.7853 -3505.8526 Loop time of 4.04111 on 1 procs for 307 steps with 2282 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 = -7592.70535447 -7638.78525233 -7638.78525233 Force two-norm initial, final = 76.1384 2.74789e-05 Force max component initial, final = 14.7721 5.43184e-06 Final line search alpha, max atom move = 1 5.43184e-06 Iterations, force evaluations = 307 603 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9591 | 3.9591 | 3.9591 | 0.0 | 97.97 Neigh | 0.008106 | 0.008106 | 0.008106 | 0.0 | 0.20 Comm | 0.044904 | 0.044904 | 0.044904 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02903 | | | 0.72 Nlocal: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13318 ave 13318 max 13318 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: 302040 ave 302040 max 302040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302040 Ave neighs/atom = 132.358 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) = 6.059 | 6.059 | 6.059 Mbytes Step Temp E_pair E_mol TotEng Press Volume 307 0 -7638.7853 0 -7638.7853 -3505.8526 38442.301 1307 0 -7638.8701 0 -7638.8701 -1643.8473 38368.002 Loop time of 13.4337 on 1 procs for 1000 steps with 2282 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 = -7638.78525233 -7638.87013409 -7638.87013438 Force two-norm initial, final = 76.0282 0.138254 Force max component initial, final = 72.3648 0.0960253 Final line search alpha, max atom move = 0.0245475 0.00235718 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.807 | 12.807 | 12.807 | 0.0 | 95.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13569 | 0.13569 | 0.13569 | 0.0 | 1.01 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4907 | | | 3.65 Nlocal: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13333 ave 13333 max 13333 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: 302292 ave 302292 max 302292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302292 Ave neighs/atom = 132.468 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 -9.23201098901316e-12 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 18 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.95414 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) = 6.196 | 6.196 | 6.196 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7638.8701 0 -7638.8701 -1643.8473 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2282 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: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13333 ave 13333 max 13333 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: 302284 ave 302284 max 302284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302284 Ave neighs/atom = 132.465 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) = 6.196 | 6.196 | 6.196 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 -7638.8701 -7638.8701 68.918745 137.76 4.0411846 -1643.8473 -1643.8473 3.6805245 -4939.2221 3.9996012 2.6378603 1273.8443 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2282 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: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13333 ave 13333 max 13333 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 151142 ave 151142 max 151142 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 302284 ave 302284 max 302284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302284 Ave neighs/atom = 132.465 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_056.1450/numatoms.out 2282 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7638.87013438351-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7638.87013438351-2282*${isolated_atom_energy} variable adjusted_pe_metal equal -7638.87013438351-2282*-9.23201098901316e-12 print "${adjusted_pe_metal} eV" file output/dump_056.1450/energy.out -7638.87013436244 eV print "${mindist_metal} Angstroms" file output/dump_056.1450/mindistance.out 2.6378603083362 Angstroms write_dump all cfg output/dump_056.1450/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_056.1450/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:17