147 lines
5.0 KiB
Plaintext
147 lines
5.0 KiB
Plaintext
LAMMPS (21 Feb 2013)
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# 3D simple cubic lattice simulation
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dimension 2
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boundary p f p
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units lj
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atom_style bond
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atom_modify sort 0 1.
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bond_style harmonic
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pair_style none
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communicate single cutoff 2.0
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# geometry
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read_data data.pos
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1 = max bonds/atom
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orthogonal box = (0 -1 -0.0001) to (16 1 0.0001)
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1 by 1 by 1 MPI processor grid
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16 atoms
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16 bonds
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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6 = max # of special neighbors
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#
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neighbor 0.5 nsq
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neigh_modify delay 0 check no
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#Langevin random seed
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variable r equal 571101
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#Langevin Temperature
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variable t equal 0.005
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# Langevin Damping variable
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variable d equal 0.5
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# time step
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timestep 0.005
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# Create velocities and equilibrate
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compute MyTemp all temp/partial 1 0 0
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velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp
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velocity all create 0.0050000000000000001041 28711 mom yes rot yes dist gaussian temp MyTemp
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velocity all set NULL 0.0 0.0 units box
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#
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fix 1 all langevin $t $t $d $r
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fix 1 all langevin 0.0050000000000000001041 $t $d $r
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fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 $d $r
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fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 0.5 $r
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fix 1 all langevin 0.0050000000000000001041 0.0050000000000000001041 0.5 571101
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fix_modify 1 temp MyTemp
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fix 2 all setforce NULL 0. 0.
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fix 3 all nve
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fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1
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fix_modify 4 temp MyTemp
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#
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# 1 2 3 4
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thermo_style custom step temp pe etotal
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thermo_modify temp MyTemp
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thermo 100
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dump 4 all atom 50000 dump_LJ_ANA.lammpstrj
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run 2000000
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WARNING: Inconsistent image flags (domain.cpp:594)
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Memory usage per processor = 1.91113 Mbytes
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Step Temp PotEng TotEng
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0 0.005 0 0.0021875
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100 0.002868961 0.00049005558 0.001745226
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200 0.0033995889 0.00054780054 0.0020351207
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300 0.0054818055 0.0010469399 0.0034452298
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400 0.0026493115 0.001228133 0.0023872068
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500 0.0042074098 0.00093834909 0.0027790909
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600 0.0057427721 0.00064844108 0.0031609039
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700 0.004921032 0.0017780884 0.0039310399
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800 0.0068003961 0.0021362756 0.0051114488
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900 0.0031879644 0.0029121839 0.0043069184
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...
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1995500 0.0052867972 0.0024314544 0.0047444281
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1995600 0.0061667626 0.00217977 0.0048777286
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1995700 0.0089339997 0.0016799003 0.0055885252
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1995800 0.0062354811 0.0027538517 0.0054818747
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1995900 0.0047870661 0.0034792552 0.0055735966
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1996000 0.0069073619 0.0026162915 0.0056382623
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1996100 0.0055415014 0.0024814778 0.0049058847
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1996200 0.0075113713 0.0025342419 0.0058204668
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1996300 0.0036175152 0.0022876907 0.0038703536
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1996400 0.0038697564 0.0019615869 0.0036546053
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1996500 0.0047409774 0.0014638951 0.0035380727
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1996600 0.0057706282 0.0016903471 0.004214997
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1996700 0.0089467126 0.0019164807 0.0058306675
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1996800 0.0049858554 0.0025648536 0.0047461653
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1996900 0.0065316826 0.0018404119 0.004698023
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1997000 0.0033658131 0.0013773556 0.0028498989
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1997100 0.0055962484 0.0014630303 0.003911389
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1997200 0.0040953065 0.001620329 0.0034120256
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1997300 0.0047377588 0.0029475742 0.0050203437
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1997400 0.0050964396 0.0032258218 0.0054555141
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1997500 0.0044928787 0.0026156731 0.0045813076
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1997600 0.0084888873 0.0020170995 0.0057309877
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1997700 0.0018489614 0.0021713336 0.0029802542
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1997800 0.00845042 0.0022370954 0.0059341542
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1997900 0.0084259507 0.0034265784 0.0071129319
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1998000 0.0035188519 0.0041636188 0.0057031165
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1998100 0.00519759 0.0029875339 0.0052614795
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1998200 0.0064780065 0.001261189 0.0040953169
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1998300 0.0043427288 0.00068946033 0.0025894042
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1998400 0.0043436101 0.00076392623 0.0026642556
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1998500 0.0048600959 0.00046276456 0.0025890565
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1998600 0.00400599 0.00083665093 0.0025892715
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1998700 0.0047726401 0.0012718685 0.0033598985
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1998800 0.0033232022 0.00096850115 0.0024224021
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1998900 0.0040710536 0.0011903803 0.0029714662
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1999000 0.0064288131 0.0011170182 0.0039296239
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1999100 0.0032828285 0.0019236157 0.0033598532
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1999200 0.0061845092 0.0016389768 0.0043446995
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1999300 0.0056427996 0.0015509544 0.0040196792
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1999400 0.0044191877 0.0013193707 0.0032527653
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1999500 0.0050278316 0.001714613 0.0039142893
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1999600 0.0088282478 0.0012904919 0.0051528503
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1999700 0.0027763532 0.0012671682 0.0024818228
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1999800 0.0031875782 0.0014186408 0.0028132062
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1999900 0.0095469347 0.0012657077 0.0054424916
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2000000 0.0050785787 0.0012610955 0.0034829737
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Loop time of 11.2467 on 1 procs for 2000000 steps with 16 atoms
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Pair time (%) = 0 (0)
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Bond time (%) = 1.87007 (16.6277)
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Neigh time (%) = 1.11974 (9.95616)
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Comm time (%) = 1.64898 (14.6619)
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Outpt time (%) = 0.0784338 (0.697395)
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Other time (%) = 6.52945 (58.0568)
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Nlocal: 16 ave 16 max 16 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4 ave 4 max 4 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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Ave special neighs/atom = 6
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Neighbor list builds = 2000000
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Dangerous builds = 0
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