LAMMPS (17 Feb 2022) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task package gpu 0 # 3d soft repulsive particles units real atom_style atomic lattice fcc 5.0 origin 0.1 0.1 0.1 Lattice spacing in x,y,z = 5 5 5 region box block -5 5 -5 5 -5 5 create_box 2 box Created orthogonal box = (-25 -25 -25) to (25 25 25) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25) create_atoms CPU = 0.000 seconds set type 1 type/ratio 2 0.5 424662346 Setting atom values ... 2000 settings made for type/ratio mass * 1.0 velocity all create 3.0 87287 pair_style python 9.0 pair_coeff * * py_pot.Harmonic A B neighbor 1.0 bin neigh_modify every 2 delay 4 check yes fix 1 all nve thermo 50 run 250 post no CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - GPU package (short-range, long-range and three-body potentials): @Article{Brown11, author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington}, title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces}, journal = {Comp.~Phys.~Comm.}, year = 2011, volume = 182, pages = {898--911} } @Article{Brown12, author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington}, title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh}, journal = {Comp.~Phys.~Comm.}, year = 2012, volume = 183, pages = {449--459} } @Article{Brown13, author = {W. M. Brown, Y. Masako}, title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials}, journal = {Comp.~Phys.~Comm.}, year = 2013, volume = 184, pages = {2785--2793} } @Article{Trung15, author = {T. D. Nguyen, S. J. Plimpton}, title = {Accelerating dissipative particle dynamics simulations for soft matter systems}, journal = {Comput.~Mater.~Sci.}, year = 2015, volume = 100, pages = {173--180} } @Article{Trung17, author = {T. D. Nguyen}, title = {GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations}, journal = {Comp.~Phys.~Comm.}, year = 2017, volume = 212, pages = {113--122} } @Article{Nikolskiy19, author = {V. Nikolskiy, V. Stegailov}, title = {GPU acceleration of four-site water models in LAMMPS}, journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic}, year = 2019 } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair python, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 423789.56 0 423825.32 249259.3 50 75.889551 422919.46 0 423824.08 248893.24 100 105.20972 422570.47 0 423824.6 250756.6 150 132.08764 422249.71 0 423824.23 251894.29 200 118.14116 422416.43 0 423824.7 252088.96 250 128.40086 422293.71 0 423824.28 252057.16 Loop time of 21.1837 on 1 procs for 250 steps with 4000 atoms write_restart repulsive.restart System init for write_restart ... generated 0 of 1 mixed pair_coeff terms from geometric mixing rule clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task package gpu 0 read_restart repulsive.restart Reading restart file ... restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022 restoring atom style atomic from restart orthogonal box = (-25 -25 -25) to (25 25 25) 1 by 1 by 1 MPI processor grid pair style python stores no restart info 4000 atoms read_restart CPU = 0.000 seconds pair_style python 10.0 pair_coeff * * py_pot.Harmonic A B shell rm -f python.dat pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A Creating table file python.dat with DATE: 2022-03-18 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair python, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: full/bin/3d bin: standard pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B Appending to table file python.dat with DATE: 2022-03-18 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B Appending to table file python.dat with DATE: 2022-03-18 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule fix 1 all nve thermo 50 run 250 post no generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 5.451 | 5.451 | 5.451 Mbytes Step Temp E_pair E_mol TotEng Press 250 128.40086 422293.71 0 423824.28 252057.16 300 119.72871 422397.4 0 423824.6 251985.11 350 124.88375 422335.77 0 423824.42 252051.28 400 121.76143 422373.11 0 423824.53 252006.39 450 125.29847 422330.9 0 423824.49 251997.23 500 126.87408 422312.08 0 423824.45 252053.51 Loop time of 28.5184 on 1 procs for 250 steps with 4000 atoms clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task package gpu 0 read_restart repulsive.restart Reading restart file ... restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022 restoring atom style atomic from restart orthogonal box = (-25 -25 -25) to (25 25 25) 1 by 1 by 1 MPI processor grid pair style python stores no restart info 4000 atoms read_restart CPU = 0.000 seconds pair_style harmonic/cut pair_coeff 1 1 0.2 9.0 pair_coeff 2 2 0.4 9.0 shell rm -f harmonic.dat pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1 Creating table file harmonic.dat with DATE: 2022-03-18 generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11 ghost atom cutoff = 11 binsize = 5.5, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair harmonic/cut, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: full/bin/3d bin: standard pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2 Appending to table file harmonic.dat with DATE: 2022-03-18 generated 1 of 1 mixed pair_coeff terms from geometric mixing rule pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2 Appending to table file harmonic.dat with DATE: 2022-03-18 generated 1 of 1 mixed pair_coeff terms from geometric mixing rule neighbor 1.0 bin neigh_modify every 2 delay 4 check yes fix 1 all nve thermo 50 run 250 post no generated 1 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes Step Temp E_pair E_mol TotEng Press 250 128.40086 422293.71 0 423824.28 252057.16 300 119.72871 422397.4 0 423824.6 251985.11 350 124.88375 422335.77 0 423824.42 252051.28 400 121.76143 422373.11 0 423824.53 252006.39 450 125.29847 422330.9 0 423824.49 251997.23 500 126.87408 422312.08 0 423824.45 252053.51 Loop time of 1.1146 on 1 procs for 250 steps with 4000 atoms clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task package gpu 0 read_restart repulsive.restart Reading restart file ... restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022 restoring atom style atomic from restart orthogonal box = (-25 -25 -25) to (25 25 25) 1 by 1 by 1 MPI processor grid pair style python stores no restart info 4000 atoms read_restart CPU = 0.000 seconds pair_style table spline 1000 pair_coeff 1 1 python.dat PYTH_A_A Reading pair table potential file python.dat with DATE: 2022-03-18 pair_coeff 1 2 python.dat PYTH_A_B Reading pair table potential file python.dat with DATE: 2022-03-18 pair_coeff 2 2 python.dat PYTH_B_B Reading pair table potential file python.dat with DATE: 2022-03-18 neighbor 1.0 bin neigh_modify every 2 delay 4 check yes fix 1 all nve thermo 50 run 250 post no generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp E_pair E_mol TotEng Press 250 128.40086 422293.71 0 423824.28 252057.14 300 119.72876 422397.4 0 423824.6 251985.09 350 124.88381 422335.77 0 423824.42 252051.26 400 121.76148 422373.11 0 423824.53 252006.37 450 125.29841 422330.9 0 423824.49 251997.2 500 126.87418 422312.08 0 423824.45 252053.48 Loop time of 0.389958 on 1 procs for 250 steps with 4000 atoms # remove temporary files shell rm repulsive.restart harmonic.dat python.dat Total wall time: 0:00:54