forked from lijiext/lammps
316 lines
9.4 KiB
Groff
316 lines
9.4 KiB
Groff
LAMMPS (12 Mar 2015)
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 all nve
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run 10
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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master list distance cutoff = 2.8
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Memory usage per processor = 2.60344 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6139081 -5.0199732
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10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638
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Loop time of 0.00962114 on 4 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00643039 (66.836)
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Neigh time (%) = 0.00174427 (18.1296)
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Comm time (%) = 0.00106865 (11.1073)
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Outpt time (%) = 3.48091e-05 (0.361798)
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Other time (%) = 0.000343025 (3.56532)
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Nlocal: 1000 ave 1013 max 989 min
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Histogram: 1 0 1 0 0 1 0 0 0 1
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Nghost: 2901 ave 2912 max 2888 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Neighs: 38996 ave 39269 max 38365 min
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Histogram: 1 0 0 0 0 0 0 0 1 2
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Total # of neighbors = 155984
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Ave neighs/atom = 38.996
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Neighbor list builds = 1
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Dangerous builds = 0
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# 1st Python function
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# example of catching a syntax error
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python simple here """
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def simple():
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import exceptions
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print "Inside simple function"
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try:
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foo += 1
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except Exception, e:
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print "FOO error:",e
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"""
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python simple invoke
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# 2nd Python function
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# example of returning the function value to a python-style variable
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# invoke it twice
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variable fact python factorial
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python factorial input 1 v_n return v_fact format ii here """
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def factorial(n):
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if n == 1: return 1
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return n*factorial(n-1)
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"""
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variable n string 10
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python factorial invoke
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print "Factorial of $n = ${fact}"
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Factorial of 10 = 3628800
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variable n string 20
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python factorial invoke
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print "Factorial of $n = ${fact}"
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Factorial of 20 = 2432902008176640000
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# 3rd Python function
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# example of calling back to LAMMPS and writing a run loop in Python
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variable cut string 0.0
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python loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
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python loop invoke
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pair_style lj/cut ${cut}
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pair_style lj/cut 1.0
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pair_coeff * * 1.0 1.0
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run 10
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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master list distance cutoff = 1.3
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Memory usage per processor = 2.63679 Mbytes
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Step Temp E_pair E_mol TotEng Press
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10 1.1259767 0.016557378 0 1.7051002 1.2784679
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20 0.87608998 0.39300382 0 1.7068103 6.0488236
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Loop time of 0.00155491 on 4 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.000403821 (25.9708)
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Neigh time (%) = 0.00049901 (32.0926)
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Comm time (%) = 0.000386357 (24.8476)
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Outpt time (%) = 2.87294e-05 (1.84766)
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Other time (%) = 0.000236988 (15.2413)
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Nlocal: 1000 ave 1015 max 987 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Nghost: 943 ave 956 max 928 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Neighs: 4431.75 ave 4498 max 4325 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Total # of neighbors = 17727
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Ave neighs/atom = 4.43175
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Neighbor list builds = 1
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Dangerous builds = 0
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pair_style lj/cut ${cut}
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pair_style lj/cut 1.1
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pair_coeff * * 1.0 1.0
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run 10
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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master list distance cutoff = 1.4
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Memory usage per processor = 2.63679 Mbytes
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Step Temp E_pair E_mol TotEng Press
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20 0.87608998 -0.33042884 0 0.9833776 8.5817494
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30 1.0155079 -0.83166219 0 0.69121891 7.9905553
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Loop time of 0.00199097 on 4 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.000789523 (39.6551)
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Neigh time (%) = 0.000541985 (27.2221)
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Comm time (%) = 0.000392973 (19.7377)
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Outpt time (%) = 2.49147e-05 (1.25138)
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Other time (%) = 0.000241578 (12.1336)
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Nlocal: 1000 ave 1019 max 983 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Nghost: 945.25 ave 962 max 925 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Neighs: 5259 ave 5343 max 5125 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Total # of neighbors = 21036
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Ave neighs/atom = 5.259
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Neighbor list builds = 1
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Dangerous builds = 0
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pair_style lj/cut ${cut}
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pair_style lj/cut 1.2
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pair_coeff * * 1.0 1.0
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run 10
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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master list distance cutoff = 1.5
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Memory usage per processor = 2.63679 Mbytes
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Step Temp E_pair E_mol TotEng Press
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30 1.0155079 -2.0616558 0 -0.53877467 7.6238572
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40 1.0490928 -2.1868324 0 -0.61358669 7.2084131
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Loop time of 0.00233454 on 4 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00106812 (45.7528)
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Neigh time (%) = 0.000583589 (24.9981)
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Comm time (%) = 0.000406563 (17.4152)
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Outpt time (%) = 2.41399e-05 (1.03403)
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Other time (%) = 0.000252128 (10.7999)
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Nlocal: 1000 ave 1013 max 984 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Nghost: 1023 ave 1035 max 1005 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Neighs: 6023.75 ave 6093 max 5953 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 24095
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Ave neighs/atom = 6.02375
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Neighbor list builds = 1
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Dangerous builds = 0
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pair_style lj/cut ${cut}
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pair_style lj/cut 1.3
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pair_coeff * * 1.0 1.0
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run 10
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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master list distance cutoff = 1.6
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Memory usage per processor = 2.63679 Mbytes
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Step Temp E_pair E_mol TotEng Press
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40 1.0490928 -3.0667608 0 -1.493515 6.2796311
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50 1.0764484 -3.1173704 0 -1.5031014 6.0850409
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Loop time of 0.00265193 on 4 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00123417 (46.5387)
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Neigh time (%) = 0.000687182 (25.9125)
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Comm time (%) = 0.000449538 (16.9514)
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Outpt time (%) = 2.40803e-05 (0.908028)
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Other time (%) = 0.000256956 (9.68938)
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Nlocal: 1000 ave 1013 max 974 min
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Histogram: 1 0 0 0 0 0 0 1 0 2
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Nghost: 1184.75 ave 1200 max 1165 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Neighs: 6784.25 ave 6922 max 6577 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Total # of neighbors = 27137
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Ave neighs/atom = 6.78425
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Neighbor list builds = 1
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Dangerous builds = 0
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pair_style lj/cut ${cut}
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pair_style lj/cut 1.4
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pair_coeff * * 1.0 1.0
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run 10
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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master list distance cutoff = 1.7
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Memory usage per processor = 2.63679 Mbytes
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Step Temp E_pair E_mol TotEng Press
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50 1.0764484 -3.6112241 0 -1.9969552 5.4223348
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60 1.1101013 -3.6616014 0 -1.9968657 5.2348251
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Loop time of 0.00285125 on 4 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00141847 (49.7491)
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Neigh time (%) = 0.000675321 (23.6851)
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Comm time (%) = 0.000490129 (17.19)
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Outpt time (%) = 2.77162e-05 (0.972071)
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Other time (%) = 0.000239611 (8.40371)
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Nlocal: 1000 ave 1016 max 981 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Nghost: 1402.25 ave 1408 max 1390 min
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Histogram: 1 0 0 0 0 0 0 1 0 2
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Neighs: 7721.75 ave 7798 max 7615 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Total # of neighbors = 30887
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Ave neighs/atom = 7.72175
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Neighbor list builds = 1
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Dangerous builds = 0
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pair_style lj/cut ${cut}
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pair_style lj/cut 1.5
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pair_coeff * * 1.0 1.0
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run 10
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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master list distance cutoff = 1.8
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Memory usage per processor = 2.63679 Mbytes
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Step Temp E_pair E_mol TotEng Press
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60 1.1101013 -3.9655053 0 -2.3007696 4.7849008
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70 1.1122144 -3.9657095 0 -2.297805 4.8014106
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Loop time of 0.00325108 on 4 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00161421 (49.6517)
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Neigh time (%) = 0.000730813 (22.4791)
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Comm time (%) = 0.000600517 (18.4713)
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Outpt time (%) = 2.87294e-05 (0.88369)
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Other time (%) = 0.000276804 (8.51423)
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Nlocal: 1000 ave 1022 max 982 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Nghost: 1595.75 ave 1604 max 1588 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 8989.75 ave 9204 max 8776 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Total # of neighbors = 35959
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Ave neighs/atom = 8.98975
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Neighbor list builds = 1
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Dangerous builds = 0
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pair_style lj/cut ${cut}
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pair_style lj/cut 1.6
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pair_coeff * * 1.0 1.0
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run 10
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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master list distance cutoff = 1.9
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Memory usage per processor = 2.63679 Mbytes
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Step Temp E_pair E_mol TotEng Press
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70 1.1122144 -4.1752688 0 -2.5073643 4.4755409
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80 1.117224 -4.1831357 0 -2.5077187 4.446079
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Loop time of 0.00360203 on 4 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00191045 (53.0381)
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Neigh time (%) = 0.000787675 (21.8676)
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Comm time (%) = 0.000629485 (17.4758)
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Outpt time (%) = 2.46167e-05 (0.683413)
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Other time (%) = 0.000249803 (6.93507)
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Nlocal: 1000 ave 1013 max 987 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Nghost: 1706 ave 1720 max 1693 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Neighs: 10809.8 ave 10831 max 10761 min
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Histogram: 1 0 0 0 0 0 0 0 1 2
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Total # of neighbors = 43239
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Ave neighs/atom = 10.8097
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Neighbor list builds = 1
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Dangerous builds = 0
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