LAMMPS (22 Jul 2025 - Development - patch_22Jul2025-8-g3b5b75d72a-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
  using 1 OpenMP thread(s) per MPI task
# LAMMPS Input File for Grain Boundaries
# Mark Tschopp, Dec2009
# Modified by PM Larsen to demonstrate the use of PTM in LAMMPS
# This file will generate a single Sigma5(310) STGB and run PTM

# ---------- Initialize Simulation ---------------------
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
  using 1 OpenMP thread(s) per MPI task
units metal
dimension 3
boundary p p p
atom_style atomic

# ---------- Create Sigma5(310) Structure ---------
lattice fcc 4.05
Lattice spacing in x,y,z = 4.05 4.05 4.05
region whole block 0.000000 12.807225 -64.0361225 64.0361225 0.000000 4.050000 units box
create_box 2 whole
Created orthogonal box = (0 -64.036123 0) to (12.807225 64.036123 4.05)
  1 by 4 by 1 MPI processor grid
region upper block INF INF 0.000000 64.0361225 INF INF units box
lattice fcc 4.05 orient x  0  3  1 orient y  0 -1  3 orient z  1  0  0
Lattice spacing in x,y,z = 5.1228898 5.1228898 4.05
create_atoms 1 region upper
Created 200 atoms
  using lattice units in orthogonal box = (0 -64.036123 0) to (12.807225 64.036123 4.05)
  create_atoms CPU = 0.001 seconds
region lower block INF INF -64.0361225 0.000000 INF INF units box
lattice fcc 4.05 orient x  0  3 -1 orient y  0  1  3 orient z  1  0  0
Lattice spacing in x,y,z = 5.1228898 5.1228898 4.05
create_atoms 2 region lower
Created 200 atoms
  using lattice units in orthogonal box = (0 -64.036123 0) to (12.807225 64.036123 4.05)
  create_atoms CPU = 0.000 seconds
group upper type 1
200 atoms in group upper
group lower type 2
200 atoms in group lower

mass 1 1.0
mass 2 1.0

# ---------- Define Interatomic Potential ---------------------
pair_style	lj/cut 2.5
pair_coeff	* * 1 1
pair_coeff	1 1 1 1.1 2.8

# ---------- Displace atoms and delete overlapping atoms ---------------------
displace_atoms upper move 0 0 0 units lattice
Displacing atoms ...
delete_atoms overlap 0.35 lower upper
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 4.8
  ghost atom cutoff = 4.8
  binsize = 2.4, bins = 6 54 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 lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Deleted 2 atoms, new total = 398

# ---------- Define PTM settings (default structures, RMSD threshold of 0.1) -------------------
compute ptm all ptm/atom default 0.1

# ---------- Dump data into Data file -------------
reset_timestep 0
dump 		1 all cfg 10000 dump.ptm_example_*.cfg mass type xs ys zs c_ptm[1] c_ptm[2] c_ptm[3] c_ptm[4] c_ptm[5] c_ptm[6] c_ptm[7]
dump_modify     1 element Al Al
run 1

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- PTM package: doi:10.1088/0965-0393/24/5/055007

@Article{larsen2016ptm,
 author={Larsen, Peter Mahler and Schmidt, S{\o}ren and
    Schi{\o}tz, Jakob},
 title={Robust Structural Identification via Polyhedral Template
    Matching},
 journal={Model.\ Simulat.\ Mater.\ Sci.\ Eng.},
 year={2016},
 number={5},
 volume={24},
 pages={055007},
 DOI = {10.1088/0965-0393/24/5/055007}}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 4.8
  ghost atom cutoff = 4.8
  binsize = 2.4, bins = 6 54 2
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
  (2) compute ptm/atom, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
WARNING: Dump 1 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220)
Per MPI rank memory allocation (min/avg/max) = 3.722 | 3.723 | 3.723 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -2.8040856      0             -2.8040856     -956.28074    
         1   0             -2.8040856      0             -2.8040856     -956.28074    
Loop time of 2.9143e-05 on 4 procs for 1 steps with 398 atoms

Performance: 2964.691 ns/day, 0.008 hours/ns, 34313.557 timesteps/s, 13.657 Matom-step/s
24.9% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.136e-06  | 4.7915e-06 | 6.382e-06  |   0.0 | 16.44
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 1.1471e-05 | 1.2158e-05 | 1.3005e-05 |   0.0 | 41.72
Output  | 4.478e-06  | 6.1992e-06 | 8.837e-06  |   0.0 | 21.27
Modify  | 2.3e-07    | 2.655e-07  | 3.3e-07    |   0.0 |  0.91
Other   |            | 5.728e-06  |            |       | 19.66

Nlocal:           99.5 ave         100 max          98 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost:          680.5 ave         688 max         674 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs:          898.5 ave         902 max         896 min
Histogram: 2 0 0 0 0 0 1 0 0 1
FullNghs:         1797 ave        1814 max        1778 min
Histogram: 1 0 0 0 0 2 0 0 0 1

Total # of neighbors = 7188
Ave neighs/atom = 18.060302
Neighbor list builds = 0
Dangerous builds = 0

print "All done"
All done
Total wall time: 0:00:00
