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 4.045259781181812*${_u_distance} variable lattice_constant_converted equal 4.045259781181812*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 12.792234635608871*${_u_distance} variable xmax_converted equal 12.792234635608871*1 variable ymin_converted equal -51.17298380221666*${_u_distance} variable ymin_converted equal -51.17298380221666*1 variable ymax_converted equal 51.17298380221666*${_u_distance} variable ymax_converted equal 51.17298380221666*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.045259781181812*${_u_distance} variable zmax_converted equal 4.045259781181812*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04525978118181 Lattice spacing in x,y,z = 4.04526 4.04526 4.04526 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 12.7922346356089 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 12.7922346356089 -51.1729838022167 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 12.7922346356089 -51.1729838022167 51.1729838022167 ${zmin_converted} ${zmax_converted} units box region whole block 0 12.7922346356089 -51.1729838022167 51.1729838022167 0 ${zmax_converted} units box region whole block 0 12.7922346356089 -51.1729838022167 51.1729838022167 0 4.04525978118181 units box create_box 2 whole Created orthogonal box = (0 -51.173 0) to (12.7922 51.173 4.04526) 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 51.1729838022167 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 3 -1 0 orient y 1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.11689 5.11689 4.04526 create_atoms 1 region upper Created 162 atoms create_atoms CPU = 0.000203133 secs group upper type 1 162 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.4230249470757705 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -51.1729838022167 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 3 1 0 orient y -1 3 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.11689 5.11689 4.04526 create_atoms 2 region lower Created 162 atoms create_atoms CPU = 6.50883e-05 secs group lower type 2 162 atoms in group lower displace_atoms lower move -1.4230249470757705 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_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*4.04525978118181 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0226298905909 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 25 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 318 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1071.8573 0 -1071.8573 7583.0494 205 0 -1081.1971 0 -1081.1971 -206.49877 Loop time of 0.556966 on 1 procs for 205 steps with 318 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1071.85734484 -1081.19711459 -1081.19711459 Force two-norm initial, final = 20.5248 6.0463e-06 Force max component initial, final = 5.26702 1.07371e-06 Final line search alpha, max atom move = 1 1.07371e-06 Iterations, force evaluations = 205 400 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54256 | 0.54256 | 0.54256 | 0.0 | 97.41 Neigh | 0.0011532 | 0.0011532 | 0.0011532 | 0.0 | 0.21 Comm | 0.0093222 | 0.0093222 | 0.0093222 | 0.0 | 1.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003932 | | | 0.71 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3981 ave 3981 max 3981 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: 44964 ave 44964 max 44964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44964 Ave neighs/atom = 141.396 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) = 4.47 | 4.47 | 4.47 Mbytes Step Temp E_pair E_mol TotEng Press Volume 205 0 -1081.1971 0 -1081.1971 -206.49877 5296.1902 1205 0 -1081.201 0 -1081.201 1037.4018 5287.9123 Loop time of 2.60432 on 1 procs for 1000 steps with 318 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1081.19711459 -1081.20095203 -1081.20095203 Force two-norm initial, final = 6.52981 0.0010232 Force max component initial, final = 5.22433 0.000819456 Final line search alpha, max atom move = 1 0.000819456 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4345 | 2.4345 | 2.4345 | 0.0 | 93.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.042697 | 0.042697 | 0.042697 | 0.0 | 1.64 Output | 4.5776e-05 | 4.5776e-05 | 4.5776e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1271 | | | 4.88 Nlocal: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4145 ave 4145 max 4145 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: 45016 ave 45016 max 45016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45016 Ave neighs/atom = 141.56 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1081.201 0 -1081.201 1037.4018 Loop time of 9.53674e-07 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4145 ave 4145 max 4145 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: 45040 ave 45040 max 45040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45040 Ave neighs/atom = 141.635 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) = 4.608 | 4.608 | 4.608 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 -1081.201 -1081.201 12.77742 102.34597 4.0436201 1037.4018 1037.4018 0.024651474 3111.9326 0.24818508 2.5807383 212.05498 Loop time of 1.90735e-06 on 1 procs for 0 steps with 318 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: 318 ave 318 max 318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4145 ave 4145 max 4145 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22520 ave 22520 max 22520 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 45040 ave 45040 max 45040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45040 Ave neighs/atom = 141.635 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_036.8699/numatoms.out 318 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1081.20095203348-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1081.20095203348-318*${isolated_atom_energy} variable adjusted_pe_metal equal -1081.20095203348-318*0 print "${adjusted_pe_metal} eV" file output/dump_036.8699/energy.out -1081.20095203348 eV print "${mindist_metal} Angstroms" file output/dump_036.8699/mindistance.out 2.58073828379039 Angstroms write_dump all cfg output/dump_036.8699/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_036.8699/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:03