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 4.03330184519291*${_u_distance}
variable lattice_constant_converted equal 4.03330184519291*1
variable xmin_converted equal 0.0*${_u_distance}
variable xmin_converted equal 0.0*1
variable xmax_converted equal 45.986716458959634*${_u_distance}
variable xmax_converted equal 45.986716458959634*1
variable ymin_converted equal -45.990749760804825*${_u_distance}
variable ymin_converted equal -45.990749760804825*1
variable ymax_converted equal 45.990749760804825*${_u_distance}
variable ymax_converted equal 45.990749760804825*1
variable zmin_converted equal 0.0*${_u_distance}
variable zmin_converted equal 0.0*1
variable zmax_converted equal 4.03330184519291*${_u_distance}
variable zmax_converted equal 4.03330184519291*1
lattice            fcc ${lattice_constant_converted}
lattice            fcc 4.03330184519291
Lattice spacing in x,y,z = 4.0333 4.0333 4.0333
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 45.9867164589596 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 45.9867164589596 -45.9907497608048 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 45.9867164589596 -45.9907497608048 45.9907497608048 ${zmin_converted} ${zmax_converted} units box
region             whole block 0 45.9867164589596 -45.9907497608048 45.9907497608048 0 ${zmax_converted} units box
region             whole block 0 45.9867164589596 -45.9907497608048 45.9907497608048 0 4.03330184519291 units box
create_box         2 whole
Created orthogonal box = (0 -45.9907 0) to (45.9867 45.9907 4.0333)
  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 45.9907497608048 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 9 -7 0 orient y 7 9 0 orient z 0 0 1
lattice            fcc 4.03330184519291 orient x 9 -7 0 orient y 7 9 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.6599 5.6599 4.0333
create_atoms       1 region upper
Created 522 atoms
  create_atoms CPU = 0.00029397 secs
group              upper type 1
522 atoms in group upper
mass               1 26.981538*${_u_mass}
mass               1 26.981538*1
displace_atoms     upper move 5.13078941294612 0 0.3333333333333333 units lattice
region             lower block INF INF ${ymin_converted}  0.0 INF INF units box
region             lower block INF INF -45.9907497608048  0.0 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 9 7 0 orient y -7 9 0 orient z 0 0 1
lattice            fcc 4.03330184519291 orient x 9 7 0 orient y -7 9 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.6599 5.6599 4.0333
create_atoms       2 region lower
Created 522 atoms
  create_atoms CPU = 0.000158787 secs
group              lower type 2
522 atoms in group lower
displace_atoms     lower move -5.13078941294612 0 -0.3333333333333333 units lattice
mass               2 26.981538*${_u_mass}
mass               2 26.981538*1
pair_style         kim EAM_Dynamo_MendelevSrolovitzAckland_2005_AlFe__MO_577453891941_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*4.03330184519291
delete_atoms       overlap ${delete_distance} all all
delete_atoms       overlap 2.01665092259646 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 = 11 22 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 24 atoms, new total = 1020
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 = 11 22 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) = 5.018 | 5.018 | 5.018 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -3411.7068            0   -3411.7068   -1609.5096 
     460            0   -3421.9496            0   -3421.9496   -7126.6499 
Loop time of 3.711 on 1 procs for 460 steps with 1020 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 = 
        -3411.70681448     -3421.94956034     -3421.94956034
  Force two-norm initial, final = 16.2702 9.28142e-10
  Force max component initial, final = 3.53346 2.02203e-10
  Final line search alpha, max atom move = 1 2.02203e-10
  Iterations, force evaluations = 460 916

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.6469     | 3.6469     | 3.6469     |   0.0 | 98.27
Neigh   | 0.004077   | 0.004077   | 0.004077   |   0.0 |  0.11
Comm    | 0.03826    | 0.03826    | 0.03826    |   0.0 |  1.03
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.02175    |            |       |  0.59

Nlocal:    1020 ave 1020 max 1020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    7236 ave 7236 max 7236 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:  144468 ave 144468 max 144468 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 144468
Ave neighs/atom = 141.635
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) = 5.018 | 5.018 | 5.018 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
     460            0   -3421.9496            0   -3421.9496   -7126.6499    17060.573 
    1460            0   -3422.1732            0   -3422.1732   -1907.6125    16944.611 
Loop time of 8.33923 on 1 procs for 1000 steps with 1020 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 = 
        -3421.94956034     -3422.17315745     -3422.17315753
  Force two-norm initial, final = 89.5775 0.0248916
  Force max component initial, final = 69.2761 0.0162024
  Final line search alpha, max atom move = 0.305196 0.00494489
  Iterations, force evaluations = 1000 1996

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 7.9965     | 7.9965     | 7.9965     |   0.0 | 95.89
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.076413   | 0.076413   | 0.076413   |   0.0 |  0.92
Output  | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.2663     |            |       |  3.19

Nlocal:    1020 ave 1020 max 1020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    7236 ave 7236 max 7236 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:  144208 ave 144208 max 144208 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 144208
Ave neighs/atom = 141.38
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 = 11 22 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) = 5.156 | 5.156 | 5.156 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -3422.1732            0   -3422.1732   -1907.6125 
Loop time of 1.19209e-06 on 1 procs for 0 steps with 1020 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:    1020 ave 1020 max 1020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    7241 ave 7241 max 7241 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:  145084 ave 145084 max 145084 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 145084
Ave neighs/atom = 142.239
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) = 5.156 | 5.156 | 5.156 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   -3422.1732   -3422.1732     45.87958      91.9815    4.0152415   -1907.6125   -1907.6125   -1.0106047   -5720.3018   -1.5251348    2.5014835    719.03855 
Loop time of 9.53674e-07 on 1 procs for 0 steps with 1020 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:    1020 ave 1020 max 1020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    7241 ave 7241 max 7241 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    72542 ave 72542 max 72542 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  145084 ave 145084 max 145084 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 145084
Ave neighs/atom = 142.239
Neighbor list builds = 0
Dangerous builds = 0
variable           num_atoms equal "count(all)"
print              "${num_atoms}" file output/dump_075.7500/numatoms.out
1020
variable  adjusted_pe_metal  equal ${pe_metal}-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -3422.1731575344-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -3422.1731575344-1020*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -3422.1731575344-1020*0
print              "${adjusted_pe_metal} eV" file output/dump_075.7500/energy.out
-3422.1731575344 eV
print              "${mindist_metal} Angstroms" file output/dump_075.7500/mindistance.out
2.5014834809659 Angstroms
write_dump         all cfg output/dump_075.7500/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_075.7500/success.out
This indicates that LAMMPS ran successfully
Total wall time: 0:00:12