LAMMPS (5 Oct 2016) # 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 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms 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 ... 1 neighbor list requests 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 Memory usage per processor = 2.60344 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 0.00927401 on 4 procs for 10 steps with 4000 atoms Performance: 465818.121 tau/day, 1078.283 timesteps/s 97.0% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0063918 | 0.0064297 | 0.0064912 | 0.1 | 69.33 Neigh | 0.00175 | 0.001769 | 0.001781 | 0.0 | 19.07 Comm | 0.00068188 | 0.00074887 | 0.0007844 | 0.1 | 8.07 Output | 1.812e-05 | 1.9312e-05 | 2.1935e-05 | 0.0 | 0.21 Modify | 0.00012898 | 0.00013059 | 0.00013304 | 0.0 | 1.41 Other | | 0.0001765 | | | 1.90 Nlocal: 1000 ave 1013 max 989 min Histogram: 1 0 1 0 0 1 0 0 0 1 Nghost: 2901 ave 2912 max 2888 min Histogram: 1 0 0 0 1 0 0 1 0 1 Neighs: 38996 ave 39269 max 38365 min Histogram: 1 0 0 0 0 0 0 0 1 2 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 """ def simple(): import exceptions print "Inside simple function" try: foo += 1 except Exception, 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 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 = 1.3 ghost atom cutoff = 1.3 binsize = 0.65 -> bins = 26 26 26 Memory usage per processor = 2.63679 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 0.00150609 on 4 procs for 10 steps with 4000 atoms Performance: 2868354.168 tau/day, 6639.709 timesteps/s 132.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.00040388 | 0.00040805 | 0.00041318 | 0.0 | 27.09 Neigh | 0.00054407 | 0.00057578 | 0.00058794 | 0.1 | 38.23 Comm | 0.00023937 | 0.00025755 | 0.00029469 | 0.1 | 17.10 Output | 1.9073e-05 | 1.9789e-05 | 2.0981e-05 | 0.0 | 1.31 Modify | 0.00012827 | 0.00012988 | 0.00013113 | 0.0 | 8.62 Other | | 0.000115 | | | 7.64 Nlocal: 1000 ave 1015 max 987 min Histogram: 1 0 0 1 0 1 0 0 0 1 Nghost: 943 ave 956 max 928 min Histogram: 1 0 0 0 1 0 1 0 0 1 Neighs: 4431.75 ave 4498 max 4325 min Histogram: 1 0 0 0 0 0 1 0 1 1 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 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 = 1.4 ghost atom cutoff = 1.4 binsize = 0.7 -> bins = 24 24 24 Memory usage per processor = 2.63679 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 0.00186372 on 4 procs for 10 steps with 4000 atoms Performance: 2317947.202 tau/day, 5365.619 timesteps/s 93.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.00075579 | 0.00077468 | 0.00078678 | 0.0 | 41.57 Neigh | 0.00057006 | 0.00057727 | 0.00058198 | 0.0 | 30.97 Comm | 0.00023437 | 0.00025171 | 0.0002768 | 0.1 | 13.51 Output | 1.7166e-05 | 1.9073e-05 | 2.1935e-05 | 0.0 | 1.02 Modify | 0.00012541 | 0.00013083 | 0.00013685 | 0.0 | 7.02 Other | | 0.0001101 | | | 5.91 Nlocal: 1000 ave 1019 max 983 min Histogram: 1 0 1 0 0 0 1 0 0 1 Nghost: 945.25 ave 962 max 925 min Histogram: 1 0 0 0 1 0 0 1 0 1 Neighs: 5259 ave 5343 max 5125 min Histogram: 1 0 0 0 0 1 0 0 0 2 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 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 = 1.5 ghost atom cutoff = 1.5 binsize = 0.75 -> bins = 23 23 23 Memory usage per processor = 2.63679 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 0.00224113 on 4 procs for 10 steps with 4000 atoms Performance: 1927595.030 tau/day, 4462.026 timesteps/s 78.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0010741 | 0.0010966 | 0.0011258 | 0.1 | 48.93 Neigh | 0.00059891 | 0.00060576 | 0.00061202 | 0.0 | 27.03 Comm | 0.00024176 | 0.00027955 | 0.00030494 | 0.2 | 12.47 Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 0.83 Modify | 0.00012755 | 0.00013041 | 0.00013423 | 0.0 | 5.82 Other | | 0.0001101 | | | 4.91 Nlocal: 1000 ave 1013 max 984 min Histogram: 1 0 0 1 0 0 0 0 1 1 Nghost: 1023 ave 1035 max 1005 min Histogram: 1 0 0 0 0 1 0 0 0 2 Neighs: 6023.75 ave 6093 max 5953 min Histogram: 2 0 0 0 0 0 0 0 0 2 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 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 = 1.6 ghost atom cutoff = 1.6 binsize = 0.8 -> bins = 21 21 21 Memory usage per processor = 2.63679 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 0.00257301 on 4 procs for 10 steps with 4000 atoms Performance: 1678965.278 tau/day, 3886.494 timesteps/s 77.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0012639 | 0.0012798 | 0.001297 | 0.0 | 49.74 Neigh | 0.00069809 | 0.00072157 | 0.00073504 | 0.1 | 28.04 Comm | 0.000283 | 0.00030494 | 0.00033665 | 0.1 | 11.85 Output | 1.6928e-05 | 1.8239e-05 | 1.9789e-05 | 0.0 | 0.71 Modify | 0.00012851 | 0.00013149 | 0.00013351 | 0.0 | 5.11 Other | | 0.000117 | | | 4.55 Nlocal: 1000 ave 1013 max 974 min Histogram: 1 0 0 0 0 0 0 1 0 2 Nghost: 1184.75 ave 1200 max 1165 min Histogram: 1 0 0 0 1 0 0 0 1 1 Neighs: 6784.25 ave 6922 max 6577 min Histogram: 1 0 0 0 0 1 0 0 1 1 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 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 = 1.7 ghost atom cutoff = 1.7 binsize = 0.85 -> bins = 20 20 20 Memory usage per processor = 2.63679 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 0.00281382 on 4 procs for 10 steps with 4000 atoms Performance: 1535281.586 tau/day, 3553.893 timesteps/s 71.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.001436 | 0.0014526 | 0.0014732 | 0.0 | 51.62 Neigh | 0.00070786 | 0.00071573 | 0.00072408 | 0.0 | 25.44 Comm | 0.00035024 | 0.00036937 | 0.00038791 | 0.1 | 13.13 Output | 1.812e-05 | 1.955e-05 | 2.2888e-05 | 0.0 | 0.69 Modify | 0.00012541 | 0.00012916 | 0.00013518 | 0.0 | 4.59 Other | | 0.0001274 | | | 4.53 Nlocal: 1000 ave 1016 max 981 min Histogram: 1 0 0 0 1 0 1 0 0 1 Nghost: 1402.25 ave 1408 max 1390 min Histogram: 1 0 0 0 0 0 0 1 0 2 Neighs: 7721.75 ave 7798 max 7615 min Histogram: 1 0 0 1 0 0 0 0 0 2 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 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 = 1.8 ghost atom cutoff = 1.8 binsize = 0.9 -> bins = 19 19 19 Memory usage per processor = 2.63679 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 0.00315809 on 4 procs for 10 steps with 4000 atoms Performance: 1367914.335 tau/day, 3166.468 timesteps/s 95.0% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0016134 | 0.0016503 | 0.0016952 | 0.1 | 52.26 Neigh | 0.00075412 | 0.00077403 | 0.00078702 | 0.0 | 24.51 Comm | 0.0003922 | 0.00044894 | 0.00050783 | 0.2 | 14.22 Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 0.59 Modify | 0.00012779 | 0.00013137 | 0.00013638 | 0.0 | 4.16 Other | | 0.0001348 | | | 4.27 Nlocal: 1000 ave 1022 max 982 min Histogram: 1 0 0 1 0 1 0 0 0 1 Nghost: 1595.75 ave 1604 max 1588 min Histogram: 1 0 0 1 0 0 1 0 0 1 Neighs: 8989.75 ave 9204 max 8776 min Histogram: 1 0 0 0 1 1 0 0 0 1 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 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 = 1.9 ghost atom cutoff = 1.9 binsize = 0.95 -> bins = 18 18 18 Memory usage per processor = 2.63679 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 0.00346923 on 4 procs for 10 steps with 4000 atoms Performance: 1245233.543 tau/day, 2882.485 timesteps/s 86.5% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0019331 | 0.001945 | 0.0019629 | 0.0 | 56.06 Neigh | 0.00082707 | 0.0008325 | 0.0008409 | 0.0 | 24.00 Comm | 0.0003984 | 0.00040597 | 0.0004189 | 0.0 | 11.70 Output | 1.8835e-05 | 1.961e-05 | 2.1935e-05 | 0.0 | 0.57 Modify | 0.00012946 | 0.00013238 | 0.00013733 | 0.0 | 3.82 Other | | 0.0001338 | | | 3.86 Nlocal: 1000 ave 1013 max 987 min Histogram: 1 0 1 0 0 0 0 1 0 1 Nghost: 1706 ave 1720 max 1693 min Histogram: 2 0 0 0 0 0 0 0 1 1 Neighs: 10809.8 ave 10831 max 10761 min Histogram: 1 0 0 0 0 0 0 0 1 2 Total # of neighbors = 43239 Ave neighs/atom = 10.8097 Neighbor list builds = 1 Dangerous builds = 0 Total wall time: 0:00:00