LAMMPS (2 Aug 2018) using 8 OpenMP thread(s) per MPI task #this is the file to calculate vacancy formation energy of carbon fiber #-----------------INITIALIZATION----------------- clear using 8 OpenMP thread(s) per MPI task units metal dimension 3 boundary p p p atom_style full #-----------------ATOM DEFINITION---------------- read_data datach4 orthogonal box = (-7.4945 -5.4525 -7.2455) to (7.5055 9.5475 7.7545) 1 by 1 by 1 MPI processor grid reading atoms ... 80 atoms 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors #-----------------FORCE FIELD-------------------- pair_style comb3 polar_off pair_coeff * * ffield.comb3 C H Reading potential file lib.comb3 with DATE: 2014-02-01 Reading potential file ffield.comb3 with DATE: 2014-02-01 neighbor 2.0 bin neigh_modify delay 10 check yes mass 1 12 mass 2 1 #---------------------------Settings---------------------------- compute csym all centro/atom fcc compute eng all pe/atom compute eatoms all reduce sum c_eng #----------------------Run Minimization------------------------- reset_timestep 0 thermo 10 thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms temp dump 1 all custom 200 dump.relax.1.* id type xs ys zs c_eng fix 1 all qeq/comb 10 1e-3 min_style cg minimize 1e-15 1e-15 5000 5000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 binsize = 6.5, bins = 3 3 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair comb3, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 20.83 | 20.83 | 20.83 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms Temp 0 -265.54386 15 15 15 -542.67105 -520.9819 -502.94301 -604.08825 -265.54386 0 10 -277.10821 15 15 15 -2623.1842 -2553.4459 -2592.0692 -2724.0376 -277.10821 0 20 -277.25393 15 15 15 -203.3725 -169.40495 -209.36976 -231.3428 -277.25393 0 30 -277.28132 15 15 15 -85.623505 24.824524 -80.25493 -201.44011 -277.28132 0 40 -277.30406 15 15 15 -102.03309 -56.982415 -81.9428 -167.17405 -277.30406 0 50 -277.31926 15 15 15 -134.21265 -83.359131 -113.53797 -205.74084 -277.31926 0 60 -277.33335 15 15 15 -90.008903 -63.849845 -44.843848 -161.33302 -277.33335 0 70 -277.36157 15 15 15 -243.11554 -208.17328 -190.62555 -330.5478 -277.36157 0 80 -277.38687 15 15 15 -143.44275 -64.599591 -113.94207 -251.7866 -277.38687 0 90 -277.40254 15 15 15 -33.113263 25.36689 -22.862587 -101.84409 -277.40254 0 100 -277.41241 15 15 15 -30.305104 10.647114 9.0619176 -110.62434 -277.41241 0 110 -277.41904 15 15 15 -90.357461 -41.257079 -45.343919 -184.47139 -277.41904 0 120 -277.42296 15 15 15 -84.124132 -20.813182 -29.557688 -202.00153 -277.42296 0 130 -277.42731 15 15 15 -57.992008 19.774748 -30.856196 -162.89458 -277.42731 0 140 -277.43239 15 15 15 -68.830539 4.96543 -50.568426 -160.88862 -277.43239 0 150 -277.43721 15 15 15 -84.37781 -4.1374735 -64.791592 -184.20436 -277.43721 0 160 -277.4433 15 15 15 -129.35742 -93.745161 -65.542126 -228.78498 -277.4433 0 170 -277.4505 15 15 15 -144.25255 -133.79039 -69.861651 -229.10561 -277.4505 0 180 -277.45644 15 15 15 -103.21489 -110.78109 -29.114094 -169.74949 -277.45644 0 190 -277.46155 15 15 15 -7.4015523 -7.1893009 64.478461 -79.493817 -277.46155 0 200 -277.46513 15 15 15 -78.487091 -72.199249 -9.7506373 -153.51139 -277.46513 0 210 -277.46828 15 15 15 -10.300258 9.7583875 57.397573 -98.056735 -277.46828 0 220 -277.47054 15 15 15 -29.534227 9.6548118 23.862706 -122.1202 -277.47054 0 230 -277.47287 15 15 15 -44.423941 16.989562 -8.07727 -142.18411 -277.47287 0 240 -277.47415 15 15 15 -42.175562 22.09663 -4.9197215 -143.7036 -277.47415 0 250 -277.4753 15 15 15 -51.485282 1.8713806 1.2761958 -157.60342 -277.4753 0 260 -277.47609 15 15 15 -55.341283 -11.267974 -2.8352686 -151.92061 -277.47609 0 270 -277.47684 15 15 15 -50.816426 -0.92178477 -1.4017341 -150.12576 -277.47684 0 280 -277.47795 15 15 15 -51.12336 6.3929795 -6.5550079 -153.20805 -277.47795 0 290 -277.47866 15 15 15 -45.256297 7.279288 -1.7675013 -141.28068 -277.47866 0 300 -277.47902 15 15 15 -49.112997 2.9012289 -3.1837712 -147.05645 -277.47902 0 310 -277.4794 15 15 15 -54.520946 -2.3771568 -6.4754714 -154.71021 -277.4794 0 320 -277.4796 15 15 15 -41.461104 12.654681 3.4776886 -140.51568 -277.4796 0 330 -277.47988 15 15 15 -33.080379 25.526196 7.1213244 -131.88866 -277.47988 0 340 -277.48022 15 15 15 -33.169545 22.344952 8.2524074 -130.10599 -277.48022 0 350 -277.48064 15 15 15 -35.324114 17.720273 6.4397595 -130.13237 -277.48064 0 360 -277.48085 15 15 15 -39.084866 13.301971 4.2897321 -134.8463 -277.48085 0 370 -277.48102 15 15 15 -41.615677 9.8274228 3.1561259 -137.83058 -277.48102 0 380 -277.48109 15 15 15 -44.569181 8.5490967 -1.0858646 -141.17077 -277.48109 0 390 -277.48128 15 15 15 -49.154631 2.3592619 -6.8921203 -142.93104 -277.48128 0 400 -277.48144 15 15 15 -46.524039 6.4045316 -4.9140499 -141.0626 -277.48144 0 410 -277.48155 15 15 15 -47.276687 3.5233702 -2.0247753 -143.32866 -277.48155 0 420 -277.48169 15 15 15 -43.797532 7.8574614 0.55953036 -139.80959 -277.48169 0 430 -277.48191 15 15 15 -35.457169 15.308194 10.538024 -132.21772 -277.48191 0 440 -277.48203 15 15 15 -43.348569 11.821675 -2.0294937 -139.83789 -277.48203 0 450 -277.48213 15 15 15 -40.488794 12.974821 1.8030242 -136.24423 -277.48213 0 460 -277.48219 15 15 15 -42.67063 5.8650795 3.5608937 -137.43786 -277.48219 0 470 -277.48224 15 15 15 -43.952751 4.643707 1.9698555 -138.47181 -277.48224 0 480 -277.48231 15 15 15 -42.543038 6.7579376 -0.13140249 -134.25565 -277.48231 0 490 -277.48234 15 15 15 -43.472166 6.1901813 1.0867872 -137.69347 -277.48234 0 500 -277.48247 15 15 15 -29.748945 21.222475 16.435125 -126.90444 -277.48247 0 510 -277.48293 15 15 15 -22.611936 33.533401 24.998322 -126.36753 -277.48293 0 520 -277.48347 15 15 15 -54.958076 -0.78122257 -5.3091221 -158.78388 -277.48347 0 530 -277.48415 15 15 15 -60.300584 -5.3010084 -8.0587911 -167.54195 -277.48415 0 540 -277.48481 15 15 15 -55.436529 1.172301 -0.84570162 -166.63619 -277.48481 0 550 -277.48563 15 15 15 -50.23872 11.576482 4.6560213 -166.94866 -277.48563 0 560 -277.48712 15 15 15 -54.039273 13.15721 6.8913235 -182.16635 -277.48712 0 570 -277.48773 15 15 15 -59.247091 9.4253024 1.0152874 -188.18186 -277.48773 0 580 -277.488 15 15 15 -60.206615 2.02884 0.39443659 -183.04312 -277.488 0 590 -277.48831 15 15 15 -57.669863 8.4327299 2.436847 -183.87917 -277.48831 0 600 -277.48853 15 15 15 -55.175665 7.9659211 4.7334508 -178.22637 -277.48853 0 610 -277.48874 15 15 15 -54.847969 5.6739863 3.0560024 -173.2739 -277.48874 0 620 -277.48881 15 15 15 -56.210694 4.5277668 0.19194136 -173.35179 -277.48881 0 630 -277.48887 15 15 15 -55.729417 4.1608908 1.4425234 -172.79166 -277.48887 0 640 -277.48892 15 15 15 -54.277594 6.4186317 1.5345467 -170.78596 -277.48892 0 650 -277.48896 15 15 15 -54.916625 7.0816489 -2.2680199 -169.5635 -277.48896 0 660 -277.48898 15 15 15 -56.057874 4.2221404 -2.7810918 -169.61467 -277.48898 0 670 -277.48901 15 15 15 -53.995108 6.8390764 -0.82020785 -168.00419 -277.48901 0 680 -277.48902 15 15 15 -54.733756 6.6398851 -1.6983497 -169.1428 -277.48902 0 690 -277.48904 15 15 15 -53.070695 7.7309224 0.78355961 -167.72657 -277.48904 0 700 -277.48905 15 15 15 -53.707754 8.0139094 -0.14571795 -168.99145 -277.48905 0 710 -277.48905 15 15 15 -56.288916 3.9624886 -1.1735558 -171.65568 -277.48905 0 720 -277.48906 15 15 15 -54.415888 6.3506854 0.87888031 -170.47723 -277.48906 0 730 -277.48906 15 15 15 -54.058085 7.2984059 0.087279858 -169.55994 -277.48906 0 740 -277.48906 15 15 15 -54.197182 7.6381821 -0.5826441 -169.64708 -277.48906 0 749 -277.48906 15 15 15 -54.290677 7.2438508 -1.1415148 -168.97437 -277.48906 0 Loop time of 5.77442 on 8 procs for 749 steps with 80 atoms 96.3% CPU use with 1 MPI tasks x 8 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -265.543863801 -277.489062326 -277.489062326 Force two-norm initial, final = 0.492178 0.00302181 Force max component initial, final = 0.0796908 0.00114149 Final line search alpha, max atom move = 0.000976562 1.11474e-006 Iterations, force evaluations = 749 1674 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5926 | 2.5926 | 2.5926 | 0.0 | 44.90 Bond | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0.016072 | 0.016072 | 0.016072 | 0.0 | 0.28 Comm | 0.014041 | 0.014041 | 0.014041 | 0.0 | 0.24 Output | 0.20775 | 0.20775 | 0.20775 | 0.0 | 3.60 Modify | 2.9339 | 2.9339 | 2.9339 | 0.0 | 50.81 Other | | 0.009989 | | | 0.17 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2035 ave 2035 max 2035 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 14566 ave 14566 max 14566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14566 Ave neighs/atom = 182.075 Ave special neighs/atom = 0 Neighbor list builds = 3 Dangerous builds = 0 run 0 Per MPI rank memory allocation (min/avg/max) = 19.7 | 19.7 | 19.7 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms Temp 749 -277.48906 15 15 15 -54.290677 7.2438508 -1.1415148 -168.97437 -277.48906 0 Loop time of 0 on 8 procs for 0 steps with 80 atoms 0.0% CPU use with 1 MPI tasks x 8 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 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 | | 0 | | | 0.00 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2035 ave 2035 max 2035 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 14602 ave 14602 max 14602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14602 Ave neighs/atom = 182.525 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 undump 1 #variable N equal count(all), counts the total number of atoms in the cell #the total number of atoms is stored to the variable N variable N equal count(all) variable No equal $N variable No equal 80 #variable Ei equal "c_eatoms" computes the initial energy of the cell system before the vacancy #E is needed to store the initial energy of the system to the variable Ei variable E equal "c_eatoms" variable Ei equal $E variable Ei equal -277.489062326138 #--------------------------------------------------------------- ###################################### # SIMULATION DONE print "All done" All done print "Total number of atoms = ${No}" Total number of atoms = 80 print "Initial energy of atoms = ${Ei}" Initial energy of atoms = -277.489062326138 Total wall time: 0:00:05