LAMMPS (30 Jul 2016) using 1 OpenMP thread(s) per MPI task ###################################################################################### variable t equal 353 variable p equal 80 variable phi equal 0.875 variable pp equal 2000 variable chemmu1 equal -0.3118625715 variable height1 equal 6.7001 variable height2 equal 50.6999 ###################################################################################### variable seed equal 31798.0000 units metal atom_style atomic boundary p p f atom_modify map array pair_style lj/cut 14.0 pair_modify mix arithmetic ###################################################################################### read_data 4.4nm_atomic.txt orthogonal box = (-1 -1 -1) to (80.822 30.778 59.251) 5 by 2 by 2 MPI processor grid WARNING: Pair style in data file differs from currently defined pair style (../read_data.cpp:528) reading atoms ... 5670 atoms #read_data 4.4nm.txt #read_restart ini_equi.restart #molecule CH4 CH4.txt group wall type 1 5643 atoms in group wall group gas type 2 27 atoms in group gas ###################################################################################### 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 -1.0001 ${height1} units box side in region 1 block -0.9999 80.8219 -0.9999 30.7779 -1.0001 6.7001 units box side in group wallbottom region 1 2838 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 59.2511 units box side in group wallup region 2 2805 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 5643 atoms in group wall set group wall type 1 5643 settings made for type group gas subtract all wall 27 atoms in group gas set group gas type 2 27 settings made for type neighbor 1.5 bin neigh_modify every 5 delay 0 compute allperatom gas stress/atom NULL compute allp gas reduce sum c_allperatom[1] c_allperatom[2] c_allperatom[3] variable allpress equal -(c_allp[1]+c_allp[2]+c_allp[3])/(3*vol) compute mdtemp gas temp ##### Initial Configuration Stabilization ######################################################## velocity gas create $t ${seed} mom yes rot yes dist gaussian velocity gas create 353 ${seed} mom yes rot yes dist gaussian velocity gas create 353 31798 mom yes rot yes dist gaussian 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 8 Memory usage per processor = 4.37135 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.6189804 2825379.9 0 2825381.1 1.1592299e+08 1 1.6189804 2824304.3 0 2824305.4 1.1587883e+08 Loop time of 0.0156581 on 20 procs for 1 steps with 5670 atoms 65.8% CPU use with 20 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 2825379.93987 2825379.93987 2824304.25026 Force two-norm initial, final = 8279.64 2059.67 Force max component initial, final = 3376.7 819.789 Final line search alpha, max atom move = 2.96148e-05 0.0242779 Iterations, force evaluations = 1 1 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.006058 | 0.0065073 | 0.0070269 | 0.3 | 41.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012112 | 0.00035716 | 0.00058055 | 0.9 | 2.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.9073e-06 | 3.3379e-06 | 4.2915e-06 | 0.0 | 0.02 Other | | 0.00879 | | | 56.14 Nlocal: 283.5 ave 315 max 259 min Histogram: 4 2 1 2 0 5 4 0 0 2 Nghost: 2161.8 ave 2241 max 2060 min Histogram: 1 2 0 1 4 4 2 1 2 3 Neighs: 109810 ave 120314 max 103430 min Histogram: 3 2 5 2 3 1 0 2 0 2 Total # of neighbors = 2196202 Ave neighs/atom = 387.337 Neighbor list builds = 0 Dangerous builds = 0 neighbor 1.5 bin neigh_modify every 1 delay 0 reset_timestep 0 ##### GCMC ################################################# #fix ID group-ID gcmc N X M type seed T mu displace keyword values fix GC gas gcmc 50 300 300 2 ${seed} $t ${chemmu1} 0.1 pressure $p fugacity_coeff ${phi} group gas region active full_energy tfac_insert 1.00 fix GC gas gcmc 50 300 300 2 31798 $t ${chemmu1} 0.1 pressure $p fugacity_coeff ${phi} group gas region active full_energy tfac_insert 1.00 fix GC gas gcmc 50 300 300 2 31798 353 ${chemmu1} 0.1 pressure $p fugacity_coeff ${phi} group gas region active full_energy tfac_insert 1.00 fix GC gas gcmc 50 300 300 2 31798 353 -0.3118625715 0.1 pressure $p fugacity_coeff ${phi} group gas region active full_energy tfac_insert 1.00 fix GC gas gcmc 50 300 300 2 31798 353 -0.3118625715 0.1 pressure 80 fugacity_coeff ${phi} group gas region active full_energy tfac_insert 1.00 fix GC gas gcmc 50 300 300 2 31798 353 -0.3118625715 0.1 pressure 80 fugacity_coeff 0.875 group gas region active full_energy tfac_insert 1.00 compute_modify mdtemp dynamic yes variable nm equal count(gas) variable totene equal etotal fix check gas ave/time 1 10 300 c_mdtemp v_allpress v_totene v_nm ave one file gcmccheck.txt fix check2 gas ave/time 1 5000 10000 c_mdtemp v_allpress v_totene v_nm ave one file ave.txt thermo 1000 thermo_style custom step v_nm c_mdtemp v_allpress etotal thermo_modify format float %12.10g timestep 0.001 run 100000 0 atoms in group FixGCMC:gcmc_exclusion_group:GC Memory usage per processor = 3.24635 Mbytes Step nm mdtemp allpress TotEng 0 27 353 31526.66465 2824305.437 1000 297 345.5220506 47.26316634 2823549.782 2000 299 368.7021723 57.08366853 2823548.105 3000 315 334.9233772 43.75051633 2823545.965 4000 348 360.5681285 73.71506522 2823546.081 5000 307 371.2120788 39.38969897 2823547.056 6000 269 363.4427868 36.37067512 2823547.212 7000 284 355.0373858 58.60949889 2823547.697 8000 307 372.6333227 50.24872603 2823547.993 9000 276 343.9738094 48.49528541 2823546.041 10000 318 347.6196799 55.9078074 2823547.18 11000 304 355.1236659 30.55513679 2823547.252 12000 292 351.8800507 54.61546122 2823547.474 13000 281 326.8358011 18.88347176 2823545.977 14000 290 330.1019998 24.74812176 2823547.237 15000 279 341.5388571 39.32903506 2823546.705 16000 324 347.110792 67.40879776 2823547.407 17000 301 310.3359695 32.71042304 2823544.149 18000 319 349.9489032 40.26138115 2823546.477 19000 296 365.110503 13.92307542 2823545.707 20000 308 352.8212341 32.03315916 2823544.798 21000 308 335.8529437 49.68849088 2823545.249 22000 288 353.8523721 30.25955596 2823545.353 23000 304 341.1018573 52.84513813 2823546.321 24000 299 359.7563674 64.07065165 2823547.402 25000 300 342.1135018 25.82728829 2823546.612 26000 304 368.4327349 66.31541693 2823547.857 27000 340 355.611401 58.13916673 2823546.08 28000 307 364.6736334 50.6011721 2823545.521 29000 294 369.2283004 44.17029234 2823545.823 30000 300 345.0538385 45.4153493 2823545.832 31000 285 358.508613 34.51731053 2823546.45 32000 307 313.2316479 22.56117762 2823545.565 33000 283 315.7701052 34.85433645 2823545.13 34000 321 362.0082439 44.29244518 2823546.829 35000 306 345.5772769 37.64090061 2823546.318 36000 289 347.4019965 38.50813381 2823545.176 37000 293 351.0194513 59.21226859 2823546.985 38000 301 339.3129265 47.59969373 2823546.39 39000 318 364.6853921 52.33461224 2823546.707 40000 293 342.9337642 30.94419014 2823546.278 41000 265 384.2903709 32.80938641 2823547.49 42000 286 367.4708233 36.98727658 2823546.611 43000 318 351.7228575 33.32205421 2823545.926 44000 309 330.6240402 31.4191558 2823544.895 45000 303 339.6269845 37.98666489 2823546.234 46000 325 338.3101837 63.64824287 2823547.603 47000 272 354.1769298 42.39643776 2823546.752 48000 283 330.9457385 44.13296404 2823546.146 49000 262 331.8465872 45.87675512 2823547.703 50000 287 341.9617335 45.21586845 2823546.796 51000 288 366.8874549 63.97766009 2823547.084 52000 290 338.2364956 31.39313633 2823545.897 53000 296 369.7086801 57.150198 2823546.362 54000 311 346.2268439 40.73592982 2823545.004 55000 326 338.2764756 47.7731511 2823545.137 56000 345 345.6652383 55.10289491 2823545.241 57000 305 346.7201172 54.67996388 2823546.047 58000 319 334.5804196 36.01930134 2823545.344 59000 295 374.6144311 43.83355419 2823547.061 60000 309 383.7104494 62.5234291 2823548.146 61000 301 375.8880287 54.88093869 2823547.108 62000 330 360.1542343 34.27066631 2823546.131 63000 317 367.2772667 53.01248871 2823547.013 64000 294 352.0649701 55.55203206 2823545.151 65000 291 341.7092477 29.57435645 2823545.469 66000 303 345.2823566 44.71571731 2823545.642 67000 330 326.206894 52.2523967 2823545.103 68000 295 369.3778012 43.67052605 2823545.917 69000 315 376.4421713 59.27405542 2823548.182 70000 328 343.4958638 55.74266974 2823545.913 71000 324 343.8388604 44.88630838 2823546.346 72000 295 339.2947411 32.39234792 2823545.905 73000 298 350.6950456 61.20414868 2823546.347 74000 289 350.046163 27.92377492 2823546.903 75000 311 308.9890527 50.27480689 2823545.085 76000 316 349.3526176 35.28066866 2823546.201 77000 301 356.7056722 37.68856055 2823545.85 78000 306 335.504971 34.06227116 2823544.942 79000 297 342.3277452 48.24487981 2823546.113 80000 295 364.6109049 64.96692872 2823547.523 81000 300 353.5380558 64.97826761 2823547.101 82000 285 361.2495822 30.48419742 2823547.415 83000 288 356.0484187 63.38529551 2823547.819 84000 308 355.556955 81.04619167 2823546.82 85000 302 373.9371621 64.44732827 2823547.866 86000 296 360.3828159 43.2698577 2823547.129 87000 303 353.6039095 43.3161598 2823546.285 88000 319 356.9420994 46.18746845 2823545.992 89000 332 351.9387905 57.34087646 2823546.399 90000 303 340.8971636 43.56327562 2823544.453 91000 324 323.6072466 50.47094048 2823544.291 92000 319 323.0581587 61.96166366 2823544.277 93000 295 335.9361494 56.64753423 2823545.159 94000 308 345.5410873 73.91006908 2823546.233 95000 284 337.592844 40.41446862 2823546.185 96000 281 360.019076 37.1078892 2823546.919 97000 283 371.8803429 43.1326758 2823546.852 98000 303 344.1401784 39.55677834 2823545.692 99000 290 331.0703176 34.48574612 2823544.53 100000 313 346.5944909 53.9444593 2823546.341 Loop time of 8051.87 on 20 procs for 100000 steps with 5956 atoms Performance: 1.073 ns/day, 22.366 hours/ns, 12.419 timesteps/s 99.7% CPU use with 20 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 280.92 | 299.01 | 322.6 | 64.6 | 3.71 Neigh | 5.485 | 5.8622 | 6.4748 | 10.3 | 0.07 Comm | 7.5455 | 24.32 | 38 | 193.2 | 0.30 Output | 0.026525 | 0.029678 | 0.034943 | 2.2 | 0.00 Modify | 7712.8 | 7718.3 | 7727 | 7.0 | 95.86 Other | | 4.398 | | | 0.05 Nlocal: 297.8 ave 331 max 275 min Histogram: 5 3 0 1 1 5 3 0 0 2 Nghost: 2338.9 ave 2412 max 2263 min Histogram: 3 1 2 1 2 4 2 1 0 4 Neighs: 114945 ave 123623 max 109703 min Histogram: 3 5 1 4 3 0 0 0 1 3 Total # of neighbors = 2298905 Ave neighs/atom = 385.981 Neighbor list builds = 1204000 Dangerous builds = 0 Total wall time: 2:14:13