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 4.049696564674378*${_u_distance} variable lattice_constant_converted equal 4.049696564674378*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 31.629141281768355*${_u_distance} variable xmax_converted equal 31.629141281768355*1 variable ymin_converted equal -63.26233226010138*${_u_distance} variable ymin_converted equal -63.26233226010138*1 variable ymax_converted equal 63.26233226010138*${_u_distance} variable ymax_converted equal 63.26233226010138*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049696564674378*${_u_distance} variable zmax_converted equal 4.049696564674378*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04969656467438 Lattice spacing in x,y,z = 4.0497 4.0497 4.0497 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 31.6291412817684 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 31.6291412817684 -63.2623322601014 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 31.6291412817684 -63.2623322601014 63.2623322601014 ${zmin_converted} ${zmax_converted} units box region whole block 0 31.6291412817684 -63.2623322601014 63.2623322601014 0 ${zmax_converted} units box region whole block 0 31.6291412817684 -63.2623322601014 63.2623322601014 0 4.04969656467438 units box create_box 2 whole Created orthogonal box = (0 -63.2623 0) to (31.6291 63.2623 4.0497) 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 63.2623322601014 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 -5 0 orient y 5 6 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 6 -5 0 orient y 5 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70362 5.70362 4.0497 create_atoms 1 region upper Created 489 atoms create_atoms CPU = 0.000319958 secs group upper type 1 489 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.514612354157994 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -63.2623322601014 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 5 0 orient y -5 6 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 6 5 0 orient y -5 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70362 5.70362 4.0497 create_atoms 2 region lower Created 489 atoms create_atoms CPU = 0.000166893 secs group lower type 2 489 atoms in group lower displace_atoms lower move -3.514612354157994 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_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*4.04969656467438 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02484828233719 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 9 34 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 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 962 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.995 | 4.995 | 4.995 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3225.5429 0 -3225.5429 -1925.251 377 0 -3235.6337 0 -3235.6337 -8442.0736 Loop time of 1.57749 on 1 procs for 377 steps with 962 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3225.54288494 -3235.63373224 -3235.63373224 Force two-norm initial, final = 14.0051 1.20183e-05 Force max component initial, final = 4.37321 4.49987e-06 Final line search alpha, max atom move = 1 4.49987e-06 Iterations, force evaluations = 377 746 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5277 | 1.5277 | 1.5277 | 0.0 | 96.84 Neigh | 0.0088639 | 0.0088639 | 0.0088639 | 0.0 | 0.56 Comm | 0.026137 | 0.026137 | 0.026137 | 0.0 | 1.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01478 | | | 0.94 Nlocal: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7003 ave 7003 max 7003 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: 107914 ave 107914 max 107914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107914 Ave neighs/atom = 112.177 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) = 4.996 | 4.996 | 4.996 Mbytes Step Temp E_pair E_mol TotEng Press Volume 377 0 -3235.6337 0 -3235.6337 -8442.0736 16206.345 1377 0 -3235.9565 0 -3235.9565 -1973.389 16071.407 Loop time of 5.07176 on 1 procs for 1000 steps with 962 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 = -3235.63373224 -3235.95649592 -3235.95649605 Force two-norm initial, final = 102.895 0.0240704 Force max component initial, final = 77.8854 0.0229268 Final line search alpha, max atom move = 1 0.0229268 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7434 | 4.7434 | 4.7434 | 0.0 | 93.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.073251 | 0.073251 | 0.073251 | 0.0 | 1.44 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2551 | | | 5.03 Nlocal: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6998 ave 6998 max 6998 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: 107208 ave 107208 max 107208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107208 Ave neighs/atom = 111.443 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 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) = 5.134 | 5.134 | 5.134 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3235.9565 0 -3235.9565 -1973.389 Loop time of 1.19209e-06 on 1 procs for 0 steps with 962 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: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7003 ave 7003 max 7003 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: 114532 ave 114532 max 114532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114532 Ave neighs/atom = 119.056 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) = 5.134 | 5.134 | 5.134 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 -3235.9565 -3235.9565 31.549968 126.52466 4.0260556 -1973.389 -1973.389 2.2798771 -5921.8101 -0.63667199 2.6186969 204.48478 Loop time of 9.53674e-07 on 1 procs for 0 steps with 962 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: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7003 ave 7003 max 7003 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57266 ave 57266 max 57266 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114532 ave 114532 max 114532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114532 Ave neighs/atom = 119.056 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_079.6111/numatoms.out 962 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3235.95649604821-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3235.95649604821-962*${isolated_atom_energy} variable adjusted_pe_metal equal -3235.95649604821-962*0 print "${adjusted_pe_metal} eV" file output/dump_079.6111/energy.out -3235.95649604821 eV print "${mindist_metal} Angstroms" file output/dump_079.6111/mindistance.out 2.61869686761383 Angstroms write_dump all cfg output/dump_079.6111/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_079.6111/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06