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 4.050000071525574*${_u_distance} variable lattice_constant_converted equal 4.050000071525574*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 47.40403547559986*${_u_distance} variable xmax_converted equal 47.40403547559986*1 variable ymin_converted equal -47.408085475671385*${_u_distance} variable ymin_converted equal -47.408085475671385*1 variable ymax_converted equal 47.408085475671385*${_u_distance} variable ymax_converted equal 47.408085475671385*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050000071525574*${_u_distance} variable zmax_converted equal 4.050000071525574*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000007152557 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 47.4040354755999 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 47.4040354755999 -47.4080854756714 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 47.4040354755999 -47.4080854756714 47.4080854756714 ${zmin_converted} ${zmax_converted} units box region whole block 0 47.4040354755999 -47.4080854756714 47.4080854756714 0 ${zmax_converted} units box region whole block 0 47.4040354755999 -47.4080854756714 47.4080854756714 0 4.05000007152557 units box create_box 2 whole Created orthogonal box = (0 -47.4081 0) to (47.404 47.4081 4.05) 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 47.4080854756714 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1 lattice fcc 4.05000007152557 orient x 11 -4 0 orient y 4 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.19022 5.19022 4.05 create_atoms 1 region upper Created 550 atoms create_atoms CPU = 0.00028491 secs group upper type 1 550 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.267114959823831 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -47.4080854756714 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 4 0 orient y -4 11 0 orient z 0 0 1 lattice fcc 4.05000007152557 orient x 11 4 0 orient y -4 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.19022 5.19022 4.05 create_atoms 2 region lower Created 550 atoms create_atoms CPU = 0.000145912 secs group lower type 2 550 atoms in group lower displace_atoms lower move -5.267114959823831 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_PunMishin_2009_NiAl__MO_751354403791_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*4.05000007152557 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500003576279 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 12 23 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1074 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 12 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.026 | 5.026 | 5.026 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3582.4945 0 -3582.4945 -3243.5322 235 0 -3594.3358 0 -3594.3358 -10716.054 Loop time of 1.65815 on 1 procs for 235 steps with 1074 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 = -3582.49449839 -3594.33575223 -3594.33575223 Force two-norm initial, final = 9.4203 9.28783e-07 Force max component initial, final = 2.49553 2.58032e-07 Final line search alpha, max atom move = 1 2.58032e-07 Iterations, force evaluations = 235 456 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6223 | 1.6223 | 1.6223 | 0.0 | 97.84 Neigh | 0.004108 | 0.004108 | 0.004108 | 0.0 | 0.25 Comm | 0.019667 | 0.019667 | 0.019667 | 0.0 | 1.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01204 | | | 0.73 Nlocal: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7398 ave 7398 max 7398 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: 148844 ave 148844 max 148844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148844 Ave neighs/atom = 138.588 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) = 5.029 | 5.029 | 5.029 Mbytes Step Temp E_pair E_mol TotEng Press Volume 235 0 -3594.3358 0 -3594.3358 -10716.054 18203.41 1235 0 -3594.9073 0 -3594.9073 -2436.0741 18009.807 Loop time of 6.784 on 1 procs for 1000 steps with 1074 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3594.33575223 -3594.90726406 -3594.90726419 Force two-norm initial, final = 148.864 0.0314764 Force max component initial, final = 112.407 0.0216559 Final line search alpha, max atom move = 0.103981 0.00225179 Iterations, force evaluations = 1000 1994 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4403 | 6.4403 | 6.4403 | 0.0 | 94.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.077807 | 0.077807 | 0.077807 | 0.0 | 1.15 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2658 | | | 3.92 Nlocal: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7655 ave 7655 max 7655 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: 149008 ave 149008 max 149008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149008 Ave neighs/atom = 138.741 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 -4.3766955338e-11 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 12 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.167 | 5.167 | 5.167 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3594.9073 0 -3594.9073 -2436.0741 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1074 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: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7705 ave 7705 max 7705 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: 149080 ave 149080 max 149080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149080 Ave neighs/atom = 138.808 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) = 5.167 | 5.167 | 5.167 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 -3594.9073 -3594.9073 47.211431 94.816171 4.0232728 -2436.0741 -2436.0741 1.9187091 -7311.6005 1.459616 2.5682321 842.05293 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1074 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: 1074 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7705 ave 7705 max 7705 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74540 ave 74540 max 74540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 149080 ave 149080 max 149080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149080 Ave neighs/atom = 138.808 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_039.9662/numatoms.out 1074 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3594.90726419383-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3594.90726419383-1074*${isolated_atom_energy} variable adjusted_pe_metal equal -3594.90726419383-1074*-4.3766955338e-11 print "${adjusted_pe_metal} eV" file output/dump_039.9662/energy.out -3594.90726414682 eV print "${mindist_metal} Angstroms" file output/dump_039.9662/mindistance.out 2.56823208092109 Angstroms write_dump all cfg output/dump_039.9662/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_039.9662/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:08