LAMMPS (29 Aug 2024 - Update 1) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task #This input file bases its pair style and pair coeff #On the paper Developing pair potentials for simulating radiation damage in complex oxides #building simulation box clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task units metal atom_style charge dimension 3 boundary p p p #reading in file for STO unitcell read_data pymatgenunitcellshift.data Reading data file ... orthogonal box = (0 0 0) to (3.905 3.905 3.905) 1 by 1 by 1 MPI processor grid reading atoms ... 5 atoms read_data CPU = 0.001 seconds #setting charge for atoms # Sr = 1 # Ti = 2 # O = 3 #set atom charge set atom 1 charge 1.84 Setting atom values ... 1 settings made for charge set atom 2 charge 2.36 Setting atom values ... 1 settings made for charge set atom 3 charge -1.40 Setting atom values ... 1 settings made for charge #interatomic interactions #Using the hybrid/overlay pair style to combine Born-Mayer's and Coulomb potentials pair_style hybrid/overlay born 3.905 coul/cut 3.905 # Specify the parameters for the Born-Mayer's part of the interaction pair_coeff 1 3 born 1769.51 0.319894 0.0 0.0 0.0 10.0 pair_coeff 2 3 born 14567.4 0.197584 0.0 0.0 0.0 10.0 pair_coeff 3 3 born 6249.17 0.231472 0.0 0.0 0.0 10.0 # Specify the parameters for the Coulomb interaction pair_coeff * * coul/cut 10.0 pair_modify shift yes #Perform an energy minimization of the system thermo 1 thermo_style custom step pe ke etotal min_style cg minimize 1.0e-8 0.0 1000 100000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 @Article{Gissinger24, pair_coeff 2 3 born 14567.4 0.197584 0.0 0.0 0.0 10.0 pair_coeff 3 3 born 6249.17 0.231472 0.0 0.0 0.0 10.0 # Specify the parameters for the Coulomb interaction pair_coeff * * coul/cut 10.0 pair_modify shift yes author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel > title = {Type Label Framework for Bonded Force Fields in LAMMPS}, journal = {J. Phys. Chem. B}, year = 2024, volume = 128, number = 13, pages = {3282–-3297} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 3 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 = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair born, perpetual, skip from (2) attributes: half, newton on pair build: skip stencil: none bin: none (2) pair coul/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.946 | 4.946 | 4.946 Mbytes Step PotEng KinEng TotEng 0 502.78902 0 502.78902 1 502.57538 0 502.57538 2 502.5707 0 502.5707 3 502.5702 0 502.5702 4 502.56804 0 502.56804 5 502.56696 0 502.56696 6 502.56611 0 502.56611 7 502.56571 0 502.56571 8 502.5655 0 502.5655 9 502.56545 0 502.56545 10 502.56542 0 502.56542 11 502.56541 0 502.56541 12 502.56541 0 502.56541 13 502.5654 0 502.5654 Loop time of 0.0062856 on 1 procs for 13 steps with 5 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 = 502.789024450652 502.565405996934 502.565404336057 Force two-norm initial, final = 5.9959971 0.21841156 Force max component initial, final = 4.3977903 0.12989438 Final line search alpha, max atom move = 4.6970741e-05 6.1012355e-06 Iterations, force evaluations = 13 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0050724 | 0.0050724 | 0.0050724 | 0.0 | 80.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007401 | 0.0007401 | 0.0007401 | 0.0 | 11.77 Output | 0.0002887 | 0.0002887 | 0.0002887 | 0.0 | 4.59 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001844 | | | 2.93 Nlocal: 5 ave 5 max 5 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2026 ave 2026 max 2026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1467 ave 1467 max 1467 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1467 Ave neighs/atom = 293.4 Neighbor list builds = 0 Dangerous builds = 0 write_data relax_unitcell_STO System init for write_data ... Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule Total wall time: 0:00:00