LAMMPS (30 Jul 2016) using 1 OpenMP thread(s) per MPI task variable t equal 353 variable height1 equal 6.7001 variable height2 equal 50.6999 variable tfac equal 1.55 ## chemical potential ############################################################## variable factor equal 0.4 variable chemmu1 equal -0.79697216*1.100*${factor} variable chemmu1 equal -0.79697216*1.100*0.4 variable chemmu2 equal -0.84520506*1.075*${factor} variable chemmu2 equal -0.84520506*1.075*0.4 variable chemmu3 equal -0.86555860*1.035*${factor} variable chemmu3 equal -0.86555860*1.035*0.4 variable chemmu4 equal -0.80546410*1.040*${factor} variable chemmu4 equal -0.80546410*1.040*0.4 variable chemmu5 equal -0.80544766*1.005*${factor} variable chemmu5 equal -0.80544766*1.005*0.4 ## fugacity coeff ##################################################### variable phi1 equal 1.0053 variable phi2 equal 0.8371 variable phi3 equal 0.7196 variable phi4 equal 0.6209 variable phi5 equal 0.5379 ########################################### units metal atom_style full boundary p p p pair_style lj/cut 14.0 pair_modify mix arithmetic bond_style harmonic angle_style harmonic dihedral_style opls read_data 4.4nm_gcmc_two_C4C5.txt orthogonal box = (-1 -1 5.7) to (80.822 30.778 51.7) 1 by 1 by 1 MPI processor grid WARNING: Pair style in data file differs from currently defined pair style (../read_data.cpp:528) reading atoms ... 1928 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom scanning dihedrals ... 1 = max dihedrals/atom reading bonds ... 35 bonds reading angles ... 24 angles reading dihedrals ... 14 dihedrals 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 2 = max # of 1-4 neighbors 4 = max # of special neighbors #read_restart ini_equi.restart ########################################### group wall type 1 1881 atoms in group wall group C1 type 2 1 atoms in group C1 group C2 id <> 1883 1884 2 atoms in group C2 group C3 id <> 1885 1887 3 atoms in group C3 group C4 id <> 1888 1903 16 atoms in group C4 group C5 id <> 1904 1928 25 atoms in group C5 ########################################### variable rxlo equal xlo+0.0001 variable rxhi equal xhi-0.0001 variable rylo equal ylo+0.0001 variable ryhi equal yhi-0.0001 variable rzlo equal zlo-0.0001 variable rzhi equal zhi+0.0001 region 1 block ${rxlo} ${rxhi} ${rylo} ${ryhi} ${rzlo} ${height1} units box side in region 1 block -0.9999 ${rxhi} ${rylo} ${ryhi} ${rzlo} ${height1} units box side in region 1 block -0.9999 80.8219 ${rylo} ${ryhi} ${rzlo} ${height1} units box side in region 1 block -0.9999 80.8219 -0.9999 ${ryhi} ${rzlo} ${height1} units box side in region 1 block -0.9999 80.8219 -0.9999 30.7779 ${rzlo} ${height1} units box side in region 1 block -0.9999 80.8219 -0.9999 30.7779 5.6999 ${height1} units box side in region 1 block -0.9999 80.8219 -0.9999 30.7779 5.6999 6.7001 units box side in group wallbottom region 1 957 atoms in group wallbottom region 2 block ${rxlo} ${rxhi} ${rylo} ${ryhi} ${height2} ${rzhi} units box side in region 2 block -0.9999 ${rxhi} ${rylo} ${ryhi} ${height2} ${rzhi} units box side in region 2 block -0.9999 80.8219 ${rylo} ${ryhi} ${height2} ${rzhi} units box side in region 2 block -0.9999 80.8219 -0.9999 ${ryhi} ${height2} ${rzhi} units box side in region 2 block -0.9999 80.8219 -0.9999 30.7779 ${height2} ${rzhi} units box side in region 2 block -0.9999 80.8219 -0.9999 30.7779 50.6999 ${rzhi} units box side in region 2 block -0.9999 80.8219 -0.9999 30.7779 50.6999 51.7001 units box side in group wallup region 2 924 atoms in group wallup region active block ${rxlo} ${rxhi} ${rylo} ${ryhi} ${height1} ${height2} units box side in region active block -0.9999 ${rxhi} ${rylo} ${ryhi} ${height1} ${height2} units box side in region active block -0.9999 80.8219 ${rylo} ${ryhi} ${height1} ${height2} units box side in region active block -0.9999 80.8219 -0.9999 ${ryhi} ${height1} ${height2} units box side in region active block -0.9999 80.8219 -0.9999 30.7779 ${height1} ${height2} units box side in region active block -0.9999 80.8219 -0.9999 30.7779 6.7001 ${height2} units box side in region active block -0.9999 80.8219 -0.9999 30.7779 6.7001 50.6999 units box side in group wall union wallbottom wallup 1881 atoms in group wall group gas subtract all wall 47 atoms in group gas neighbor 1.5 bin neigh_modify every 5 delay 0 velocity gas create 353 31798 mom yes rot yes dist gaussian compute mdtemp gas temp compute_modify mdtemp dynamic yes reset_timestep 0 ###### EQUILIBRATE ####################################################### fix setforce wall setforce 0.0 0.0 0.0 minimize 1.0e-3 1.0e-3 10000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75 -> bins = 11 5 6 Memory usage per processor = 10.8552 Mbytes Step Temp E_pair E_mol TotEng Press 0 8.4265698 945392.08 1.1146834 945395.3 50815710 1 8.4265698 945392.08 0.57309505 945394.75 50815711 Loop time of 0.0453591 on 1 procs for 1 steps with 1928 atoms 97.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 945393.197495 945393.197495 945392.655951 Force two-norm initial, final = 8.32557 2.14961 Force max component initial, final = 2.01157 0.647016 Final line search alpha, max atom move = 0.0497125 0.0321647 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044465 | 0.044465 | 0.044465 | 0.0 | 98.03 Bond | 0.00025606 | 0.00025606 | 0.00025606 | 0.0 | 0.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020504 | 0.00020504 | 0.00020504 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.9802e-05 | 2.9802e-05 | 2.9802e-05 | 0.0 | 0.07 Other | | 0.0004034 | | | 0.89 Nlocal: 1928 ave 1928 max 1928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8394 ave 8394 max 8394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 533690 ave 533690 max 533690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533690 Ave neighs/atom = 276.81 Ave special neighs/atom = 0.0757261 Neighbor list builds = 0 Dangerous builds = 0 fix mdrun gas nvt temp 353 353 10.0 fix_modify mdrun temp mdtemp WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1377) thermo 1000 timestep 0.001 run 5000 Neighbor list info ... 1 neighbor list requests update every 5 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75 -> bins = 11 5 6 Memory usage per processor = 14.2302 Mbytes Step Volume mdtemp allpress C1press C2press C3press C4press C5press 1 119606.4177 353 13.27177158 1.145139765 -1.469672229 1.736844979 7.230419482 4.629039587 1000 119606.4177 340.8227473 -56.849747 1.145201866 -3.656613772 -3.19328235 -13.48785429 -37.65719845 2000 119606.4177 342.6004322 -36.63093754 1.14080918 4.658382582 1.296567175 -32.80187803 -10.92481845 3000 119606.4177 305.2063835 -5.808881784 1.117772788 -3.281776846 3.146956459 -14.05321455 7.261380369 4000 119606.4177 302.9366964 -25.70690418 1.408708367 -3.231587248 -3.793758912 -11.02354151 -9.066724872 5000 119606.4177 422.7015095 37.56427439 1.083389008 8.124908072 3.863362245 17.48250763 7.010107436 5001 119606.4177 430.8105337 35.36891717 1.083473415 8.309972925 3.747800284 16.74910257 5.478567979 Loop time of 109.727 on 1 procs for 5000 steps with 1928 atoms Performance: 3.937 ns/day, 6.096 hours/ns, 45.568 timesteps/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 94.294 | 94.294 | 94.294 | 0.0 | 85.93 Bond | 0.97912 | 0.97912 | 0.97912 | 0.0 | 0.89 Neigh | 0.72447 | 0.72447 | 0.72447 | 0.0 | 0.66 Comm | 0.36995 | 0.36995 | 0.36995 | 0.0 | 0.34 Output | 0.014854 | 0.014854 | 0.014854 | 0.0 | 0.01 Modify | 13.223 | 13.223 | 13.223 | 0.0 | 12.05 Other | | 0.1223 | | | 0.11 Nlocal: 1928 ave 1928 max 1928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8400 ave 8400 max 8400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 534730 ave 534730 max 534730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 534730 Ave neighs/atom = 277.35 Ave special neighs/atom = 0.0757261 Neighbor list builds = 84 Dangerous builds = 0