LAMMPS (2 Jun 2022) ######################################################################################## # Input file for simulating (rigid) CO2 molecules # Reference : # [Potoff and J.I. Siepmann, Vapor-liquid equilibria of # mixtures containing alkanes, carbon dioxide and # nitrogen AIChE J., 47,1676-1682 (2001)]. #------------------------ # Global model settings #------------------------ units real atom_style full boundary p p p pair_style lj/cut/coul/long 14 pair_modify mix arithmetic tail yes kspace_style ewald 0.0001 bond_style harmonic angle_style harmonic #------------------------ # Constants and variables #------------------------ variable Temp equal 338.0 # in K variable Pres equal 1 # in atm variable spacing index 15.0 # [Ang] - lattice spaing variable Ninvt equal 10000 # Initialize the NVT ensemble (very small timesteps) variable Npnvt equal 500000 # Production the NVT ensemble variable Nf equal 500 # rate of outputting to the log file variable lbox index 30.0 # [ang] - box dimensions in angstroms #--------------------------------------------- # Box, start molecules on simple cubic lattice #--------------------------------------------- lattice sc ${spacing} lattice sc 15.0 Lattice spacing in x,y,z = 15 15 15 region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box region box block 0 30.0 0 ${lbox} 0 ${lbox} units box region box block 0 30.0 0 30.0 0 ${lbox} units box region box block 0 30.0 0 30.0 0 30.0 units box create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 Created orthogonal box = (0 0 0) to (30 30 30) 1 by 2 by 2 MPI processor grid molecule co2mol CO2.txt Read molecule template co2mol: 1 molecules 0 fragments 3 atoms with max type 2 2 bonds with max type 1 1 angles with max type 1 0 dihedrals with max type 0 0 impropers with max type 0 create_atoms 0 box mol co2mol 464563 units box Created 24 atoms using box units in orthogonal box = (0 0 0) to (30 30 30) create_atoms CPU = 0.001 seconds #----------------------- # rigid CO2 TraPPE model #----------------------- pair_coeff 1 1 0.053649 2.8 pair_coeff 2 2 0.156973 3.05 bond_coeff 1 0 1.16 angle_coeff 1 0 180 #------- # Masses #------- mass 1 12.0107 mass 2 15.9994 #------------ # MD settings #------------ group co2 type 1 2 24 atoms in group co2 neighbor 2.0 bin neigh_modify every 1 delay 0 check yes timestep 1.0 run_style verlet #------------------------ # NVT simulations - rigid #------------------------ fix myrigidnvt co2 rigid/nvt/small molecule temp ${Temp} ${Temp} 10 fix myrigidnvt co2 rigid/nvt/small molecule temp 338 ${Temp} 10 fix myrigidnvt co2 rigid/nvt/small molecule temp 338 338 10 create bodies CPU = 0.000 seconds 8 rigid bodies with 24 atoms 1.16 = max distance from body owner to body atom # fix myrigidnvt co2 rigid/nvt molecule temp ${Temp} ${Temp} 10 #------- # Output #------- dump trjec all custom 1 movie1.lammpstrj id type x y z vx vy vz compute 1 co2 ke compute 2 co2 ke/rigid myrigidnvt # (scalar) sum of the translational kinetic energy of rigid bodies compute 3 co2 erotate/rigid myrigidnvt # (scalar) sum of the rotational kinetic energy of rigid bodies compute 4 co2 temp thermo_style custom step temp pe c_1 c_2 c_3 c_4 ke press vol density thermo ${Nf} thermo 500 thermo_modify temp 4 WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:520) #-------------------- # Run (Initialization) #-------------------- # initialize to imposed temperature velocity all create ${Temp} 54654 velocity all create 338 54654 WARNING: Cannot count rigid body degrees-of-freedom before bodies are fully initialized (../fix_rigid_small.cpp:1137) run 0 Ewald initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.13673848 estimated absolute RMS force accuracy = 0.033750362 estimated relative force accuracy = 0.00010163821 KSpace vectors: actual max1d max3d = 61 3 171 kxmax kymax kzmax = 3 3 3 Generated 1 of 1 mixed pair_coeff terms from arithmetic 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 = 16 ghost atom cutoff = 16 binsize = 8, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 18.64 | 18.64 | 18.64 Mbytes Step Temp PotEng c_1 c_2 c_3 c_4 KinEng Press Volume Density 0 386.52184 -0.059595169 14.209828 8.3526807 5.857147 386.52184 14.209828 839.75329 27000 0.021653182 Loop time of 9.795e-07 on 4 procs for 0 steps with 24 atoms 76.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 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 | | 9.795e-07 | | |100.00 Nlocal: 6 ave 7 max 5 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 212 ave 213 max 211 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 53.5 ave 72 max 34 min Histogram: 1 0 0 0 1 0 1 0 0 1 Total # of neighbors = 214 Ave neighs/atom = 8.9166667 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 velocity all scale ${Temp} velocity all scale 338 WARNING: Changing velocities of atoms in rigid bodies. This has no effect unless rigid bodies are rebuild (../velocity.cpp:72) velocity all zero linear # set box momentum to zero WARNING: Changing velocities of atoms in rigid bodies. This has no effect unless rigid bodies are rebuild (../velocity.cpp:72) timestep 0.01 run ${Ninvt} run 10000 Ewald initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:342) G vector (1/distance) = 0.13673848 estimated absolute RMS force accuracy = 0.033750362 estimated relative force accuracy = 0.00010163821 KSpace vectors: actual max1d max3d = 61 3 171 kxmax kymax kzmax = 3 3 3 Generated 1 of 1 mixed pair_coeff terms from arithmetic mixing rule Per MPI rank memory allocation (min/avg/max) = 18.64 | 18.64 | 18.64 Mbytes Step Temp PotEng c_1 c_2 c_3 c_4 KinEng Press Volume Density 0 338 -0.059595169 12.426003 7.3041308 5.1218727 338 12.426003 20.474227 27000 0.021653182 500 344.38988 -0.020382233 12.660917 7.4792673 5.1816495 344.38988 12.660917 25.784741 27000 0.021653182 1000 365.18024 -0.060708136 13.425239 8.0506226 5.3746167 365.18024 13.425239 43.642819 27000 0.021653182 1500 410.81449 -0.061916274 15.102906 9.3094145 5.7934916 410.81449 15.102906 80.870194 27000 0.021653182 2000 510.641 -0.063301871 18.772861 12.064919 6.7079417 510.641 18.772861 128.74552 27000 0.021653182 2500 597.15842 -0.025550641 21.953529 14.390648 7.5628803 597.15842 21.953529 31.027884 27000 0.021653182 3000 520.41159 0.012758911 19.13206 12.014533 7.1175264 520.41159 19.13206 -124.04475 27000 0.021653182 3500 367.83756 0.032184324 13.522931 8.0398572 5.4830742 367.83756 13.522931 -107.95756 27000 0.021653182 4000 278.02543 0.071279665 10.221139 6.268224 3.952915 278.02543 10.221139 -32.462766 27000 0.021653182 4500 247.31665 0.070794198 9.0921823 5.8871696 3.2050126 247.31665 9.0921823 13.303005 27000 0.021653182 5000 258.0015 0.050753827 9.4849927 6.3343157 3.1506771 258.0015 9.4849927 52.961997 27000 0.021653182 5500 318.03775 0.01070549 11.692125 7.6095927 4.0825322 318.03775 11.692125 90.756313 27000 0.021653182 6000 484.60472 0.010043347 17.81568 9.556589 8.2590913 484.60472 17.81568 100.81448 27000 0.021653182 6500 605.0093 0.048994793 22.242153 11.205909 11.036243 605.0093 22.242153 60.980581 27000 0.021653182 7000 545.78169 0.047977705 20.064749 11.197806 8.8669434 545.78169 20.064749 -39.271775 27000 0.021653182 7500 378.09718 0.086481312 13.900109 7.8649585 6.0351508 378.09718 13.900109 -199.15152 27000 0.021653182 8000 252.40797 0.12563316 9.279356 4.9082138 4.3711422 252.40797 9.279356 -82.45863 27000 0.021653182 8500 218.63585 0.12529207 8.0377804 4.3009387 3.7368418 218.63585 8.0377804 9.3996342 27000 0.021653182 9000 233.03874 0.12489426 8.5672785 4.803061 3.7642175 233.03874 8.5672785 73.951858 27000 0.021653182 9500 292.6288 0.12437347 10.758007 6.3126964 4.4453108 292.6288 10.758007 124.10104 27000 0.021653182 10000 392.56745 0.14336974 14.432084 8.3251959 6.1068884 392.56745 14.432084 107.19765 27000 0.021653182 Loop time of 0.395569 on 4 procs for 10000 steps with 24 atoms Performance: 21.842 ns/day, 1.099 hours/ns, 25280.042 timesteps/s 98.5% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0020598 | 0.0029224 | 0.0035388 | 1.0 | 0.74 Bond | 0.0011003 | 0.0012413 | 0.0014254 | 0.3 | 0.31 Kspace | 0.052243 | 0.052933 | 0.053759 | 0.3 | 13.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.061882 | 0.063621 | 0.06444 | 0.4 | 16.08 Output | 0.09183 | 0.10279 | 0.12224 | 3.6 | 25.99 Modify | 0.1472 | 0.16598 | 0.17582 | 2.8 | 41.96 Other | | 0.006081 | | | 1.54 Nlocal: 6 ave 7 max 5 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 212 ave 213 max 211 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 53.5 ave 72 max 34 min Histogram: 1 0 0 0 1 0 1 0 0 1 Total # of neighbors = 214 Ave neighs/atom = 8.9166667 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0