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 1 by 1 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 = 2.69271 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 0.03213 on 1 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.0242701 (75.5371)
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Neigh time (%) = 0.006531 (20.3268)
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Comm time (%) = 0.000502825 (1.56497)
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Outpt time (%) = 2.09808e-05 (0.0652998)
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Other time (%) = 0.00080514 (2.50588)
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5841 ave 5841 max 5841 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 155984 ave 155984 max 155984 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 = 2.78761 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 0.00451207 on 1 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00158691 (35.1704)
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Neigh time (%) = 0.00194287 (43.0594)
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Comm time (%) = 0.000257015 (5.69617)
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Outpt time (%) = 2.09808e-05 (0.464993)
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Other time (%) = 0.000704288 (15.609)
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2083 ave 2083 max 2083 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 17727 ave 17727 max 17727 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 = 2.78761 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 0.00607896 on 1 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00298262 (49.0646)
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Neigh time (%) = 0.00210714 (34.6629)
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Comm time (%) = 0.000262499 (4.31816)
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Outpt time (%) = 2.00272e-05 (0.329451)
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Other time (%) = 0.000706673 (11.6249)
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2087 ave 2087 max 2087 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 21036 ave 21036 max 21036 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 = 2.78761 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 0.00735807 on 1 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00416398 (56.5906)
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Neigh time (%) = 0.00219989 (29.8976)
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Comm time (%) = 0.000262022 (3.56101)
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Outpt time (%) = 1.90735e-05 (0.259218)
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Other time (%) = 0.00071311 (9.69153)
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2250 ave 2250 max 2250 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 24095 ave 24095 max 24095 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 = 2.78761 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 0.0085659 on 1 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00486517 (56.7969)
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Neigh time (%) = 0.00266886 (31.1568)
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Comm time (%) = 0.000301838 (3.52371)
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Outpt time (%) = 2.00272e-05 (0.233801)
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Other time (%) = 0.000710011 (8.2888)
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2572 ave 2572 max 2572 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 27137 ave 27137 max 27137 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 = 2.78761 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 0.0091939 on 1 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00552583 (60.1032)
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Neigh time (%) = 0.00259781 (28.2558)
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Comm time (%) = 0.000323296 (3.51642)
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Outpt time (%) = 2.00272e-05 (0.217831)
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Other time (%) = 0.000726938 (7.90675)
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3013 ave 3013 max 3013 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 30887 ave 30887 max 30887 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 = 2.78761 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 0.0102301 on 1 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00630403 (61.6225)
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Neigh time (%) = 0.00282717 (27.6359)
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Comm time (%) = 0.000349283 (3.41428)
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Outpt time (%) = 2.00272e-05 (0.195768)
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Other time (%) = 0.000729561 (7.13154)
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3388 ave 3388 max 3388 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 35959 ave 35959 max 35959 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 = 2.78761 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 0.011508 on 1 procs for 10 steps with 4000 atoms
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Pair time (%) = 0.00736189 (63.972)
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Neigh time (%) = 0.00303006 (26.3301)
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Comm time (%) = 0.000365019 (3.17187)
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Outpt time (%) = 2.00272e-05 (0.174028)
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Other time (%) = 0.000730991 (6.35203)
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3612 ave 3612 max 3612 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 43239 ave 43239 max 43239 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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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