LAMMPS (23 Oct 2017) using 1 OpenMP thread(s) per MPI task # GCMC for CO2 molecular fluid, rigid/small/nvt dynamics # Rigid CO2 TraPPE model # [Potoff and J.I. Siepmann, Vapor-liquid equilibria of # mixtures containing alkanes, carbon dioxide and # nitrogen AIChE J., 47,1676-1682 (2001)]. # variables available on command line variable mu index -8.1 variable disp index 0.5 variable temp index 338.0 variable lbox index 10.0 variable spacing index 5.0 # 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 # box, start molecules on simple cubic lattice lattice sc ${spacing} lattice sc 5.0 Lattice spacing in x,y,z = 5 5 5 region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box region box block 0 10.0 0 ${lbox} 0 ${lbox} units box region box block 0 10.0 0 10.0 0 ${lbox} units box region box block 0 10.0 0 10.0 0 10.0 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 (10 10 10) 1 by 2 by 2 MPI processor grid molecule co2mol CO2.txt Read molecule co2mol: 3 atoms with 2 types 2 bonds with 1 types 1 angles with 1 types 0 dihedrals with 0 types 0 impropers with 0 types create_atoms 0 box mol co2mol 464563 units box Created 24 atoms Time spent = 0.00261331 secs # 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 10 check yes velocity all create ${temp} 54654 velocity all create 338.0 54654 timestep 1.0 # rigid constraints with thermostat fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol 8 rigid bodies with 24 atoms 1.16 = max distance from body owner to body atom fix_modify myrigidnvt dynamic/dof no # gcmc variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt # atom counts variable carbon atom "type==1" variable oxygen atom "type==2" group carbon dynamic all var carbon dynamic group carbon defined group oxygen dynamic all var oxygen dynamic group oxygen defined variable nC equal count(carbon) variable nO equal count(oxygen) # output variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) compute_modify thermo_temp dynamic/dof yes thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO thermo 1000 # run run 20000 Ewald initialization ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.164636 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445) 0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 binsize = 8, bins = 2 2 2 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 15.41 | 15.41 | 15.41 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0 8 16 WARNING: Using kspace solver on system with no charge (../kspace.cpp:289) 1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0 5 10 2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0 3 6 3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0 13 26 4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28 5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0 14 28 6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0 15 30 7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0 15 30 8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0 13 26 9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0 15 30 10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0 14 28 11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0 15 30 12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0 15 30 13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0 15 30 14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0 14 28 15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0 14 28 16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0 14 28 17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0 14 28 18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0 15 30 19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0 15 30 20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0 15 30 Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 timesteps/s 98.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1687 | 1.6702 | 2.1864 | 30.8 | 5.15 Bond | 0.018828 | 0.020035 | 0.020975 | 0.6 | 0.06 Kspace | 0.57506 | 1.0931 | 1.5898 | 37.7 | 3.37 Neigh | 0.068863 | 0.069524 | 0.070128 | 0.2 | 0.21 Comm | 2.0735 | 2.0865 | 2.0979 | 0.7 | 6.43 Output | 0.0025017 | 0.0025966 | 0.0027781 | 0.2 | 0.01 Modify | 27.335 | 27.344 | 27.363 | 0.2 | 84.27 Other | | 0.1621 | | | 0.50 Nlocal: 11.25 ave 14 max 8 min Histogram: 1 0 0 0 0 1 1 0 0 1 Nghost: 2639.75 ave 2656 max 2617 min Histogram: 1 0 0 0 0 0 2 0 0 1 Neighs: 4320 ave 5824 max 2201 min Histogram: 1 0 0 0 0 0 1 1 0 1 Total # of neighbors = 17280 Ave neighs/atom = 384 Ave special neighs/atom = 2 Neighbor list builds = 20394 Dangerous builds = 0 Total wall time: 0:00:32