LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # 2d circle of particles inside a box with LJ walls variable b index 0 variable x index 50 variable y index 20 variable d index 20 variable v index 5 variable w index 2 units lj dimension 2 atom_style bond boundary f f p lattice hex 0.85 Lattice spacing in x,y,z = 1.1655347 2.0187654 1.1655347 region box block 0 $x 0 $y -0.5 0.5 region box block 0 50 0 $y -0.5 0.5 region box block 0 50 0 20 -0.5 0.5 create_box 1 box bond/types 1 extra/bond/per/atom 6 Created orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737) 2 by 1 by 1 MPI processor grid region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2) region circle sphere 11 6.7735026918962581988 0.0 10 create_atoms 1 region circle Created 361 atoms using lattice units in orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737) create_atoms CPU = 0.001 seconds mass 1 1.0 velocity all create 0.5 87287 loop geom velocity all set $v $w 0 sum yes velocity all set 5 $w 0 sum yes velocity all set 5 2 0 sum yes pair_style lj/cut 2.5 pair_coeff 1 1 10.0 1.0 2.5 bond_style harmonic bond_coeff 1 10.0 1.2 # need to preserve 1-3, 1-4 pairwise interactions during hard collisions special_bonds lj/coul 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 1 1 0 = max # of 1-2 neighbors 1 = max # of special neighbors special bonds CPU = 0.000 seconds create_bonds many all all 1 1.0 1.5 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4, bins = 42 29 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command create_bonds, occasional attributes: full, newton on pair build: full/bin stencil: full/bin/2d bin: standard (2) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/2d bin: standard Added 1014 bonds, new total = 1014 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 1 1 6 = max # of 1-2 neighbors 6 = max # of special neighbors special bonds CPU = 0.000 seconds neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 all nve fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5 fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5 fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5 fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5 comm_style tiled comm_modify cutoff 10.0 # because bonds stretch a long ways fix 10 all balance 50 0.9 rcb #compute 1 all property/atom proc #variable p atom (c_1%10)+1 #dump 2 all custom 50 tmp.dump id v_p x y z #dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02 #variable colors string # "red green blue yellow white # purple pink orange lime gray" #dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors} thermo_style custom step temp epair press f_10[3] f_10 thermo 100 timestep 0.001 run 10000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 10 binsize = 1.4, bins = 42 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/2d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.157 | 5.167 | 5.178 Mbytes Step Temp E_pair Press f_10[3] f_10 0 25.701528 -2.2032569 3.1039469 2 1.0193906 100 25.57187 -2.2902218 2.9990153 1.0193906 1.0027701 200 25.532511 -2.5273097 2.8286231 1.0304709 1.0027701 300 25.860246 -3.0674998 2.6725358 1.0138504 1.0027701 400 26.628011 -4.394738 2.6618897 1.0138504 1.0083102 500 27.627309 -6.2305012 2.6564278 1.0138504 1.0027701 600 28.881803 -8.2757766 2.8249236 1.0138504 1.0027701 700 29.941402 -9.9816088 2.9828232 1.0138504 1.0027701 800 31.118457 -12.199787 3.2044549 1.0249307 1.0083102 900 32.393498 -14.204491 2.9496587 1.0304709 1.0027701 1000 33.392657 -15.747519 3.1613807 1.0249307 1.0027701 1100 34.671769 -17.728904 3.019138 1.0193906 1.0083102 1200 35.632627 -19.846347 3.1061176 1.0193906 1.0083102 1300 36.77272 -21.156179 3.2353009 1.0415512 1.0027701 1400 38.241608 -22.744765 4.1163075 1.0193906 1.0027701 1500 40.072478 -25.139827 5.3032535 1.0304709 1.0027701 1600 40.665382 -25.901697 5.4330761 1.0304709 1.0027701 1700 40.957034 -26.28667 7.1881521 1.0360111 1.0027701 1800 41.536831 -27.393841 6.6814405 1.0470914 1.0027701 1900 41.952676 -28.123051 7.4683871 1.0360111 1.0027701 2000 42.201937 -28.685743 7.4624285 1.0304709 1.0027701 2100 41.509082 -27.909225 6.8666951 1.0304709 1.0083102 2200 40.794911 -27.085519 5.2599455 1.0415512 1.0027701 2300 38.74971 -25.146012 4.2936194 1.0360111 1.0083102 2400 38.418073 -24.593601 3.1418121 1.0470914 1.0027701 2500 36.932581 -23.407617 1.9397617 1.0304709 1.0027701 2600 35.979152 -23.066707 2.1676871 1.0415512 1.0027701 2700 35.848339 -22.556586 2.079815 1.0526316 1.0027701 2800 35.796197 -22.092919 2.6843042 1.0470914 1.0027701 2900 35.752758 -21.6603 2.4924275 1.0360111 1.0083102 3000 36.548479 -21.940002 2.8478206 1.0304709 1.0027701 3100 36.74473 -22.072441 3.7028736 1.0193906 1.0027701 3200 36.633543 -22.568923 3.7319143 1.0249307 1.0083102 3300 37.175051 -23.069268 3.5045201 1.0193906 1.0027701 3400 36.942892 -23.480254 3.1212991 1.0193906 1.0027701 3500 37.813564 -24.659011 3.6045332 1.0138504 1.0027701 3600 37.856787 -24.954353 4.3062815 1.0249307 1.0027701 3700 38.543481 -25.054481 4.7177629 1.0304709 1.0027701 3800 39.011196 -25.760455 4.9664492 1.0304709 1.0027701 3900 38.784228 -25.618896 4.944851 1.0304709 1.0027701 4000 39.348833 -26.615389 4.8191233 1.0304709 1.0027701 4100 39.242191 -26.754066 4.7960336 1.0249307 1.0027701 4200 38.989902 -26.741978 3.7980048 1.0415512 1.0027701 4300 38.726515 -25.916493 3.7176038 1.0304709 1.0027701 4400 38.720441 -25.549542 3.3956415 1.0470914 1.0027701 4500 38.22257 -25.122141 4.5771547 1.0304709 1.0083102 4600 38.217511 -25.390842 4.4896706 1.0360111 1.0027701 4700 39.121636 -26.227786 4.9811267 1.0415512 1.0083102 4800 39.306166 -26.700977 4.9963051 1.0249307 1.0027701 4900 38.909059 -25.799524 6.1957543 1.0692521 1.0027701 5000 38.778196 -26.491002 5.6393984 1.0526316 1.0027701 5100 38.587868 -27.253335 5.5460314 1.0415512 1.0027701 5200 38.686438 -27.40612 5.5186442 1.0249307 1.0027701 5300 37.986414 -26.049806 5.3696903 1.0304709 1.0027701 5400 37.111804 -26.019738 4.2114526 1.0415512 1.0083102 5500 36.62295 -25.592884 5.1349 1.0415512 1.0027701 5600 36.087987 -25.398454 4.4963434 1.0249307 1.0083102 5700 34.435409 -24.548062 3.5310124 1.0249307 1.0027701 5800 33.18681 -22.76355 3.2061242 1.0470914 1.0027701 5900 32.57428 -21.832024 3.2865828 1.0193906 1.0027701 6000 30.557555 -20.714816 4.2280358 1.0304709 1.0083102 6100 31.893092 -21.235479 4.5931729 1.0304709 1.0027701 6200 31.577761 -21.222778 4.1847871 1.0415512 1.0027701 6300 32.003743 -20.825156 5.6968257 1.0526316 1.0027701 6400 32.073012 -20.877815 7.3062956 1.0360111 1.0027701 6500 31.588306 -21.556202 5.7846536 1.0138504 1.0027701 6600 32.453985 -21.478064 4.8089249 1.0083102 1.0027701 6700 31.269576 -21.24005 4.0540095 1.0193906 1.0027701 6800 31.548438 -21.335039 3.767158 1.0138504 1.0027701 6900 31.249216 -20.689547 4.5435057 1.0083102 1.0027701 7000 31.72893 -20.373971 6.0204212 1.0249307 1.0027701 7100 30.888569 -19.028984 5.2458824 1.0027701 1.0027701 7200 30.747229 -19.579694 3.2582453 1.0138504 1.0083102 7300 28.339584 -19.225504 3.1235472 1.0193906 1.0027701 7400 26.754307 -18.557545 1.3860606 1.0193906 1.0083102 7500 26.559389 -17.395026 1.7206081 1.0138504 1.0083102 7600 26.227728 -16.755138 2.1148459 1.0193906 1.0027701 7700 26.361463 -15.711397 2.5458994 1.0138504 1.0027701 7800 26.081484 -16.032712 0.70050048 1.0138504 1.0027701 7900 24.660082 -15.079215 1.1999533 1.0138504 1.0027701 8000 24.448184 -14.668849 0.63886653 1.0138504 1.0083102 8100 24.198589 -15.157555 0.12256041 1.0027701 1.0027701 8200 24.764129 -14.876966 0.97060609 1.0249307 1.0083102 8300 25.33268 -14.891698 1.6089548 1.0083102 1.0027701 8400 24.992342 -14.652659 1.3317376 1.0138504 1.0027701 8500 25.115045 -14.683247 0.98361969 1.0138504 1.0027701 8600 24.954894 -14.451543 1.2228755 1.0083102 1.0027701 8700 24.51303 -14.159235 0.75345783 1.0249307 1.0083102 8800 22.697326 -13.254743 1.2913804 1.0138504 1.0027701 8900 22.868775 -13.677092 -0.048154854 1.0083102 1.0027701 9000 25.269332 -13.649225 1.0337367 1.0083102 1.0083102 9100 24.184813 -12.826606 1.1160895 1.0360111 1.0027701 9200 23.664589 -13.449013 0.031451624 1.0193906 1.0083102 9300 23.944566 -13.401803 0.20095909 1.0193906 1.0027701 9400 24.146696 -12.879011 0.89518549 1.0249307 1.0027701 9500 25.383214 -13.411768 0.95798595 1.0304709 1.0027701 9600 25.248933 -13.838658 0.45253554 1.0304709 1.0027701 9700 24.38613 -13.123006 1.5446061 1.0138504 1.0027701 9800 25.743921 -13.610838 1.2556191 1.0083102 1.0027701 9900 26.468479 -13.72971 2.3998562 1.0249307 1.0027701 10000 26.338099 -14.82183 1.5233934 1.0193906 1.0027701 Loop time of 0.372607 on 2 procs for 10000 steps with 361 atoms Performance: 2318795.909 tau/day, 26837.916 timesteps/s, 9.688 Matom-step/s 96.0% CPU use with 2 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13582 | 0.14029 | 0.14475 | 1.2 | 37.65 Bond | 0.035027 | 0.035038 | 0.035049 | 0.0 | 9.40 Neigh | 0.085828 | 0.08675 | 0.087673 | 0.3 | 23.28 Comm | 0.05562 | 0.05851 | 0.061399 | 1.2 | 15.70 Output | 0.0010102 | 0.0011746 | 0.0013391 | 0.5 | 0.32 Modify | 0.029008 | 0.02926 | 0.029512 | 0.1 | 7.85 Other | | 0.02159 | | | 5.79 Nlocal: 180.5 ave 181 max 180 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 166.5 ave 170 max 163 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 1628.5 ave 1652 max 1605 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 3257 Ave neighs/atom = 9.0221607 Ave special neighs/atom = 5.6177285 Neighbor list builds = 1208 Dangerous builds = 0 Total wall time: 0:00:00