LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt with Python functions added units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 10 0 10 0 10 create_box 1 box Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms Time spent = 0.00072813 secs mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 all nve run 10 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 = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.721 | 3.721 | 3.721 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6139081 -5.0199732 10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638 Loop time of 0.0312054 on 1 procs for 10 steps with 4000 atoms Performance: 138437.508 tau/day, 320.457 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022328 | 0.022328 | 0.022328 | 0.0 | 71.55 Neigh | 0.0073318 | 0.0073318 | 0.0073318 | 0.0 | 23.50 Comm | 0.0006578 | 0.0006578 | 0.0006578 | 0.0 | 2.11 Output | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.09 Modify | 0.00057721 | 0.00057721 | 0.00057721 | 0.0 | 1.85 Other | | 0.0002832 | | | 0.91 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 155984 ave 155984 max 155984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155984 Ave neighs/atom = 38.996 Neighbor list builds = 1 Dangerous builds = 0 # 1st Python function # example of catching a syntax error python simple here """ from __future__ import print_function def simple(): foo = 0 print("Inside simple function") try: foo += 1 except Exception as e: print("FOO error:", e) """ python simple invoke # 2nd Python function # example of returning the function value to a python-style variable # invoke it twice variable fact python factorial python factorial input 1 v_n return v_fact format ii here """ def factorial(n): if n == 1: return 1 return n*factorial(n-1) """ variable n string 10 python factorial invoke print "Factorial of $n = ${fact}" Factorial of 10 = 3628800 variable n string 20 python factorial invoke print "Factorial of $n = ${fact}" Factorial of 20 = 2432902008176640000 # 3rd Python function # example of calling back to LAMMPS and writing a run loop in Python variable cut string 0.0 python loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py python loop invoke pair_style lj/cut ${cut} pair_style lj/cut 1.0 pair_coeff * * 1.0 1.0 run 10 Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 10 1.1259767 0.016557378 0 1.7051002 1.2784679 20 0.87608998 0.39300382 0 1.7068103 6.0488236 Loop time of 0.00488138 on 1 procs for 10 steps with 4000 atoms Performance: 884995.276 tau/day, 2048.600 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0017166 | 0.0017166 | 0.0017166 | 0.0 | 35.17 Neigh | 0.0020256 | 0.0020256 | 0.0020256 | 0.0 | 41.50 Comm | 0.00028539 | 0.00028539 | 0.00028539 | 0.0 | 5.85 Output | 2.6703e-05 | 2.6703e-05 | 2.6703e-05 | 0.0 | 0.55 Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 11.76 Other | | 0.0002532 | | | 5.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2083 ave 2083 max 2083 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17727 ave 17727 max 17727 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17727 Ave neighs/atom = 4.43175 Neighbor list builds = 1 Dangerous builds = 0 pair_style lj/cut ${cut} pair_style lj/cut 1.1 pair_coeff * * 1.0 1.0 run 10 Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 20 0.87608998 -0.33042884 0 0.9833776 8.5817494 30 1.0155079 -0.83166219 0 0.69121891 7.9905553 Loop time of 0.00647616 on 1 procs for 10 steps with 4000 atoms Performance: 667061.565 tau/day, 1544.124 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0030439 | 0.0030439 | 0.0030439 | 0.0 | 47.00 Neigh | 0.002295 | 0.002295 | 0.002295 | 0.0 | 35.44 Comm | 0.00028467 | 0.00028467 | 0.00028467 | 0.0 | 4.40 Output | 2.3842e-05 | 2.3842e-05 | 2.3842e-05 | 0.0 | 0.37 Modify | 0.0005753 | 0.0005753 | 0.0005753 | 0.0 | 8.88 Other | | 0.0002534 | | | 3.91 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2087 ave 2087 max 2087 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21036 ave 21036 max 21036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21036 Ave neighs/atom = 5.259 Neighbor list builds = 1 Dangerous builds = 0 pair_style lj/cut ${cut} pair_style lj/cut 1.2 pair_coeff * * 1.0 1.0 run 10 Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 30 1.0155079 -2.0616558 0 -0.53877467 7.6238572 40 1.0490928 -2.1868324 0 -0.61358669 7.2084131 Loop time of 0.00802207 on 1 procs for 10 steps with 4000 atoms Performance: 538514.378 tau/day, 1246.561 timesteps/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0044219 | 0.0044219 | 0.0044219 | 0.0 | 55.12 Neigh | 0.0024219 | 0.0024219 | 0.0024219 | 0.0 | 30.19 Comm | 0.00030112 | 0.00030112 | 0.00030112 | 0.0 | 3.75 Output | 2.5749e-05 | 2.5749e-05 | 2.5749e-05 | 0.0 | 0.32 Modify | 0.00059366 | 0.00059366 | 0.00059366 | 0.0 | 7.40 Other | | 0.0002577 | | | 3.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2250 ave 2250 max 2250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24095 ave 24095 max 24095 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24095 Ave neighs/atom = 6.02375 Neighbor list builds = 1 Dangerous builds = 0 pair_style lj/cut ${cut} pair_style lj/cut 1.3 pair_coeff * * 1.0 1.0 run 10 Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 40 1.0490928 -3.0667608 0 -1.493515 6.2796311 50 1.0764484 -3.1173704 0 -1.5031014 6.0850409 Loop time of 0.00908327 on 1 procs for 10 steps with 4000 atoms Performance: 475599.593 tau/day, 1100.925 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0049157 | 0.0049157 | 0.0049157 | 0.0 | 54.12 Neigh | 0.0029771 | 0.0029771 | 0.0029771 | 0.0 | 32.78 Comm | 0.00033617 | 0.00033617 | 0.00033617 | 0.0 | 3.70 Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.25 Modify | 0.00057578 | 0.00057578 | 0.00057578 | 0.0 | 6.34 Other | | 0.0002553 | | | 2.81 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2572 ave 2572 max 2572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27137 ave 27137 max 27137 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27137 Ave neighs/atom = 6.78425 Neighbor list builds = 1 Dangerous builds = 0 pair_style lj/cut ${cut} pair_style lj/cut 1.4 pair_coeff * * 1.0 1.0 run 10 Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 50 1.0764484 -3.6112241 0 -1.9969552 5.4223348 60 1.1101013 -3.6616014 0 -1.9968657 5.2348251 Loop time of 0.0096159 on 1 procs for 10 steps with 4000 atoms Performance: 449256.007 tau/day, 1039.944 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0054793 | 0.0054793 | 0.0054793 | 0.0 | 56.98 Neigh | 0.0028973 | 0.0028973 | 0.0028973 | 0.0 | 30.13 Comm | 0.00038075 | 0.00038075 | 0.00038075 | 0.0 | 3.96 Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.24 Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 5.97 Other | | 0.0002615 | | | 2.72 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3013 ave 3013 max 3013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30887 ave 30887 max 30887 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30887 Ave neighs/atom = 7.72175 Neighbor list builds = 1 Dangerous builds = 0 pair_style lj/cut ${cut} pair_style lj/cut 1.5 pair_coeff * * 1.0 1.0 run 10 Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 60 1.1101013 -3.9655053 0 -2.3007696 4.7849008 70 1.1122144 -3.9657095 0 -2.297805 4.8014106 Loop time of 0.0107083 on 1 procs for 10 steps with 4000 atoms Performance: 403424.172 tau/day, 933.852 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0062652 | 0.0062652 | 0.0062652 | 0.0 | 58.51 Neigh | 0.0031667 | 0.0031667 | 0.0031667 | 0.0 | 29.57 Comm | 0.00041771 | 0.00041771 | 0.00041771 | 0.0 | 3.90 Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.21 Modify | 0.0005734 | 0.0005734 | 0.0005734 | 0.0 | 5.35 Other | | 0.0002627 | | | 2.45 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3388 ave 3388 max 3388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35959 ave 35959 max 35959 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35959 Ave neighs/atom = 8.98975 Neighbor list builds = 1 Dangerous builds = 0 pair_style lj/cut ${cut} pair_style lj/cut 1.6 pair_coeff * * 1.0 1.0 run 10 Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 70 1.1122144 -4.1752688 0 -2.5073643 4.4755409 80 1.117224 -4.1831357 0 -2.5077187 4.446079 Loop time of 0.0121632 on 1 procs for 10 steps with 4000 atoms Performance: 355170.795 tau/day, 822.155 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0074623 | 0.0074623 | 0.0074623 | 0.0 | 61.35 Neigh | 0.0033951 | 0.0033951 | 0.0033951 | 0.0 | 27.91 Comm | 0.00043678 | 0.00043678 | 0.00043678 | 0.0 | 3.59 Output | 2.408e-05 | 2.408e-05 | 2.408e-05 | 0.0 | 0.20 Modify | 0.00057578 | 0.00057578 | 0.00057578 | 0.0 | 4.73 Other | | 0.0002692 | | | 2.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3612 ave 3612 max 3612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43239 ave 43239 max 43239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43239 Ave neighs/atom = 10.8097 Neighbor list builds = 1 Dangerous builds = 0 Total wall time: 0:00:00