LAMMPS (2 Aug 2018) using 8 OpenMP thread(s) per MPI task #this is the file to calculate the enegy of a carbon sheet #-----------------INITIALIZATION----------------- clear using 8 OpenMP thread(s) per MPI task units metal dimension 3 boundary s s s atom_style charge #-----------------ATOM DEFINITION---------------- read_data data orthogonal box = (-1.22802 0 0) to (2.45605 4.254 3.35) 1 by 1 by 1 MPI processor grid reading atoms ... 16 atoms #-----------------FORCE FIELD-------------------- pair_style comb3 polar_off pair_coeff * * ffield.comb3 C 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 #---------------------------Settings---------------------------- 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 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 = 1 1 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair comb3, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.539 | 7.539 | 7.539 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms 0 -78.871476 3.6848067 4.254851 3.3506699 35145.36 61988.672 32413.449 11033.958 -78.871476 10 -79.491652 3.6848067 4.254851 3.3506699 5798.7612 -806.88275 10838.951 7364.2155 -79.491652 20 -79.495585 3.6848067 4.254851 3.3506699 2320.108 9447.1638 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0.20762189 -0.29062248 0.069928528 -79.510289 1560 -79.510289 4.3366667 4.9252453 4.2692906 0.054063185 0.058503068 -0.10891299 0.21259948 -79.510289 1570 -79.510289 4.3366667 4.9252453 4.2692906 -0.085899128 -0.5271579 0.10200513 0.16745539 -79.510289 1580 -79.510289 4.3366667 4.9252453 4.2692906 -0.37210783 -0.61033216 -0.49826105 -0.0077302847 -79.510289 1590 -79.510289 4.3366667 4.9252453 4.2692906 -0.043625814 -0.022974855 -0.10487281 -0.0030297821 -79.510289 1600 -79.510289 4.3366667 4.9252453 4.2692906 0.10952213 0.02434591 0.052405563 0.25181491 -79.510289 1610 -79.510289 4.3366667 4.9252453 4.2692906 0.11625772 -0.51159506 0.23710133 0.62326689 -79.510289 1620 -79.510289 4.3366667 4.9252453 4.2692906 -0.06543251 -0.23280262 0.2385814 -0.2020763 -79.510289 1630 -79.510289 4.3366667 4.9252453 4.2692906 -0.14462649 0.048927421 -0.24714306 -0.23566383 -79.510289 1640 -79.510289 4.3366667 4.9252453 4.2692906 0.011169896 0.11696088 -0.0032517489 -0.080199447 -79.510289 1650 -79.510289 4.3366667 4.9252453 4.2692906 0.048110448 -0.015224802 0.044166313 0.11538983 -79.510289 1660 -79.510289 4.3366667 4.9252453 4.2692906 0.025707787 -0.024432233 0.031867731 0.069687861 -79.510289 1665 -79.510289 4.3366667 4.9252453 4.2692906 -0.00014198268 -0.003744876 0.0028289223 0.00049000569 -79.510289 Loop time of 0.507497 on 8 procs for 1665 steps with 16 atoms 27.7% CPU use with 1 MPI tasks x 8 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -78.8714755988 -79.5102891695 -79.5102891695 Force two-norm initial, final = 7.73844 5.90624e-007 Force max component initial, final = 2.83691 1.69734e-007 Final line search alpha, max atom move = 1 1.69734e-007 Iterations, force evaluations = 1665 3339 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15947 | 0.15947 | 0.15947 | 0.0 | 31.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0.31995 | 0.31995 | 0.31995 | 0.0 | 63.05 Modify | 0.018045 | 0.018045 | 0.018045 | 0.0 | 3.56 Other | | 0.01003 | | | 1.98 Nlocal: 16 ave 16 max 16 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 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: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240 Ave neighs/atom = 15 Neighbor list builds = 1 Dangerous builds = 0 run 0 Per MPI rank memory allocation (min/avg/max) = 7.538 | 7.538 | 7.538 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms 1665 -79.510289 4.3518312 4.9189871 4.3233383 -0.00013989689 -0.003689862 0.002787364 0.00048280727 -79.510289 Loop time of 0 on 8 procs for 0 steps with 16 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 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: 16 ave 16 max 16 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 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: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240 Ave neighs/atom = 15 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 16 #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 -79.5102891695014 #--------------------------------------------------------------- ###################################### # SIMULATION DONE print "All done" All done print "Total number of atoms = ${No}" Total number of atoms = 16 print "Initial energy of atoms = ${Ei}" Initial energy of atoms = -79.5102891695014 Total wall time: 0:00:00