397 lines
14 KiB
Plaintext
397 lines
14 KiB
Plaintext
LAMMPS (5 Oct 2016)
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# 3d Lennard-Jones melt with Python functions added
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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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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4 -> bins = 12 12 12
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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 0.00927401 on 4 procs for 10 steps with 4000 atoms
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Performance: 465818.121 tau/day, 1078.283 timesteps/s
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97.0% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0063918 | 0.0064297 | 0.0064912 | 0.1 | 69.33
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Neigh | 0.00175 | 0.001769 | 0.001781 | 0.0 | 19.07
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Comm | 0.00068188 | 0.00074887 | 0.0007844 | 0.1 | 8.07
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Output | 1.812e-05 | 1.9312e-05 | 2.1935e-05 | 0.0 | 0.21
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Modify | 0.00012898 | 0.00013059 | 0.00013304 | 0.0 | 1.41
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Other | | 0.0001765 | | | 1.90
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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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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.3
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ghost atom cutoff = 1.3
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binsize = 0.65 -> bins = 26 26 26
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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 0.00150609 on 4 procs for 10 steps with 4000 atoms
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Performance: 2868354.168 tau/day, 6639.709 timesteps/s
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132.8% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.00040388 | 0.00040805 | 0.00041318 | 0.0 | 27.09
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Neigh | 0.00054407 | 0.00057578 | 0.00058794 | 0.1 | 38.23
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Comm | 0.00023937 | 0.00025755 | 0.00029469 | 0.1 | 17.10
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Output | 1.9073e-05 | 1.9789e-05 | 2.0981e-05 | 0.0 | 1.31
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Modify | 0.00012827 | 0.00012988 | 0.00013113 | 0.0 | 8.62
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Other | | 0.000115 | | | 7.64
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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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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.4
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ghost atom cutoff = 1.4
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binsize = 0.7 -> bins = 24 24 24
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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 0.00186372 on 4 procs for 10 steps with 4000 atoms
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Performance: 2317947.202 tau/day, 5365.619 timesteps/s
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93.9% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.00075579 | 0.00077468 | 0.00078678 | 0.0 | 41.57
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Neigh | 0.00057006 | 0.00057727 | 0.00058198 | 0.0 | 30.97
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Comm | 0.00023437 | 0.00025171 | 0.0002768 | 0.1 | 13.51
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Output | 1.7166e-05 | 1.9073e-05 | 2.1935e-05 | 0.0 | 1.02
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Modify | 0.00012541 | 0.00013083 | 0.00013685 | 0.0 | 7.02
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Other | | 0.0001101 | | | 5.91
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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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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.5
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ghost atom cutoff = 1.5
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binsize = 0.75 -> bins = 23 23 23
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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 0.00224113 on 4 procs for 10 steps with 4000 atoms
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Performance: 1927595.030 tau/day, 4462.026 timesteps/s
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78.1% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0010741 | 0.0010966 | 0.0011258 | 0.1 | 48.93
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Neigh | 0.00059891 | 0.00060576 | 0.00061202 | 0.0 | 27.03
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Comm | 0.00024176 | 0.00027955 | 0.00030494 | 0.2 | 12.47
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Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 0.83
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Modify | 0.00012755 | 0.00013041 | 0.00013423 | 0.0 | 5.82
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Other | | 0.0001101 | | | 4.91
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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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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.6
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ghost atom cutoff = 1.6
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binsize = 0.8 -> bins = 21 21 21
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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 0.00257301 on 4 procs for 10 steps with 4000 atoms
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Performance: 1678965.278 tau/day, 3886.494 timesteps/s
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77.7% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0012639 | 0.0012798 | 0.001297 | 0.0 | 49.74
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Neigh | 0.00069809 | 0.00072157 | 0.00073504 | 0.1 | 28.04
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Comm | 0.000283 | 0.00030494 | 0.00033665 | 0.1 | 11.85
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Output | 1.6928e-05 | 1.8239e-05 | 1.9789e-05 | 0.0 | 0.71
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Modify | 0.00012851 | 0.00013149 | 0.00013351 | 0.0 | 5.11
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Other | | 0.000117 | | | 4.55
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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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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.7
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ghost atom cutoff = 1.7
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binsize = 0.85 -> bins = 20 20 20
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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 0.00281382 on 4 procs for 10 steps with 4000 atoms
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Performance: 1535281.586 tau/day, 3553.893 timesteps/s
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71.1% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.001436 | 0.0014526 | 0.0014732 | 0.0 | 51.62
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Neigh | 0.00070786 | 0.00071573 | 0.00072408 | 0.0 | 25.44
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Comm | 0.00035024 | 0.00036937 | 0.00038791 | 0.1 | 13.13
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Output | 1.812e-05 | 1.955e-05 | 2.2888e-05 | 0.0 | 0.69
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Modify | 0.00012541 | 0.00012916 | 0.00013518 | 0.0 | 4.59
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Other | | 0.0001274 | | | 4.53
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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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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.8
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ghost atom cutoff = 1.8
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binsize = 0.9 -> bins = 19 19 19
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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 0.00315809 on 4 procs for 10 steps with 4000 atoms
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Performance: 1367914.335 tau/day, 3166.468 timesteps/s
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95.0% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0016134 | 0.0016503 | 0.0016952 | 0.1 | 52.26
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Neigh | 0.00075412 | 0.00077403 | 0.00078702 | 0.0 | 24.51
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Comm | 0.0003922 | 0.00044894 | 0.00050783 | 0.2 | 14.22
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Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 0.59
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Modify | 0.00012779 | 0.00013137 | 0.00013638 | 0.0 | 4.16
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Other | | 0.0001348 | | | 4.27
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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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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.9
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ghost atom cutoff = 1.9
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binsize = 0.95 -> bins = 18 18 18
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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 0.00346923 on 4 procs for 10 steps with 4000 atoms
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Performance: 1245233.543 tau/day, 2882.485 timesteps/s
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86.5% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0019331 | 0.001945 | 0.0019629 | 0.0 | 56.06
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Neigh | 0.00082707 | 0.0008325 | 0.0008409 | 0.0 | 24.00
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Comm | 0.0003984 | 0.00040597 | 0.0004189 | 0.0 | 11.70
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Output | 1.8835e-05 | 1.961e-05 | 2.1935e-05 | 0.0 | 0.57
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Modify | 0.00012946 | 0.00013238 | 0.00013733 | 0.0 | 3.82
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Other | | 0.0001338 | | | 3.86
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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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Total wall time: 0:00:00
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