refactor and apply clang-format
- replace file reader code using TextFileReader and ValueTokenizer - replace traversing list of fixes with accessor functions - enable and apply clang-format - add examples for reading rigid bodies from file
This commit is contained in:
Axel Kohlmeyer
15
examples/rigid/connected-bodies.dat
Normal file
15
examples/rigid/connected-bodies.dat
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@ -0,0 +1,15 @@
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# Body definition file for POEMS fix
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# 1 chain of 9 connected bodies
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# Format
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# Body-ID Body-Type Atom-ID1 Atom-ID2 ...
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1 1 1 2 3 4 5 6 7 8 9
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2 2 9 10 11 12 13 14 15 16 17 18
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3 1 18 19 20 21 22 23 24 25 26 27
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4 2 27 28 29 30 31 32 33 34 35 36
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5 3 36 37 38 39 40 41 42 43 44 45
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6 1 45 46 47 48 49 50 51 52 53 54
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7 2 54 55 56 57 58 59 60 61 62 63
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8 1 63 64 65 66 67 68 69 70 71 72
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9 2 72 73 74 75 76 77 78 79 80 81
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17
examples/rigid/connected-bodies2.dat
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17
examples/rigid/connected-bodies2.dat
Normal file
@ -0,0 +1,17 @@
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# Body definition file for POEMS fix
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# 2 chains of 4 and 5 connected rigid bodies, respectively
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# Format
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# Body-ID Body-Type Atom-ID1 Atom-ID2 ...
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# chain 1
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1 1 1 2 3 4 5 6 7 8 9
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2 2 9 10 11 12 13 14 15 16 17 18
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3 1 18 19 20 21 22 23 24 25 26 27
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4 2 27 28 29 30 31 32 33 34 35 36
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# chain 2
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5 3 37 38 39 40 41 42 43 44 45
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6 1 45 46 47 48 49 50 51 52 53 54
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7 2 54 55 56 57 58 59 60 61 62 63
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8 1 63 64 65 66 67 68 69 70 71 72
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9 2 72 73 74 75 76 77 78 79 80 81
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@ -9,21 +9,6 @@ read_data data.rigid
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velocity all create 100.0 4928459
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# unconnected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 10 18
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#group clump3 id <> 19 27
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#group clump4 id <> 28 36
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#group clump5 id <> 37 45
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#group clump6 id <> 46 54
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#group clump7 id <> 55 63
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#group clump8 id <> 64 72
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#group clump9 id <> 73 81
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#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
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# clump6 clump7 clump8 clump9
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# 1 chain of connected bodies
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group clump1 id <> 1 9
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@ -39,21 +24,6 @@ group clump9 id <> 72 81
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fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
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clump6 clump7 clump8 clump9
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# 2 chains of connected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 37 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#fix 1 all poems group clump1 clump2 clump3 clump4
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#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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@ -9,36 +9,6 @@ read_data data.rigid
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velocity all create 100.0 4928459
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# unconnected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 10 18
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#group clump3 id <> 19 27
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#group clump4 id <> 28 36
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#group clump5 id <> 37 45
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#group clump6 id <> 46 54
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#group clump7 id <> 55 63
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#group clump8 id <> 64 72
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#group clump9 id <> 73 81
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#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
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# clump6 clump7 clump8 clump9
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# 1 chain of connected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 36 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
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# clump6 clump7 clump8 clump9
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# 2 chains of connected bodies
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group clump1 id <> 1 9
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@ -51,8 +21,10 @@ group clump7 id <> 54 63
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group clump8 id <> 63 72
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group clump9 id <> 72 81
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fix 1 all poems group clump1 clump2 clump3 clump4
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fix 2 all poems group clump5 clump6 clump7 clump8 clump9
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#fix 1 all poems group clump1 clump2 clump3 clump4
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#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
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fix 1 all poems group clump1 clump2 clump3 clump4 &
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clump5 clump6 clump7 clump8 clump9
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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50
examples/rigid/in.rigid.poems3
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50
examples/rigid/in.rigid.poems3
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@ -0,0 +1,50 @@
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# Simple rigid body system
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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read_data data.rigid
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velocity all create 100.0 4928459
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# unconnected bodies
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group clump1 id <> 1 9
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group clump2 id <> 10 18
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group clump3 id <> 19 27
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group clump4 id <> 28 36
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group clump5 id <> 37 45
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group clump6 id <> 46 54
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group clump7 id <> 55 63
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group clump8 id <> 64 72
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group clump9 id <> 73 81
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fix 1 all poems file unconnected-bodies.dat
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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#dump 1 all atom 50 dump.rigid.poems
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#dump 2 all image 100 image.*.jpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 100 movie.mpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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timestep 0.0001
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thermo 50
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run 10000
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50
examples/rigid/in.rigid.poems4
Normal file
50
examples/rigid/in.rigid.poems4
Normal file
@ -0,0 +1,50 @@
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# Simple rigid body system
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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read_data data.rigid
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velocity all create 100.0 4928459
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# 1 chain of connected bodies
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group clump1 id <> 1 9
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group clump2 id <> 9 18
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group clump3 id <> 18 27
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group clump4 id <> 27 36
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group clump5 id <> 36 45
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group clump6 id <> 45 54
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group clump7 id <> 54 63
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group clump8 id <> 63 72
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group clump9 id <> 72 81
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fix 1 all poems file connected-bodies.dat
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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#dump 1 all atom 50 dump.rigid.poems
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#dump 2 all image 100 image.*.jpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 100 movie.mpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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timestep 0.0001
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thermo 50
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run 10000
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51
examples/rigid/in.rigid.poems5
Normal file
51
examples/rigid/in.rigid.poems5
Normal file
@ -0,0 +1,51 @@
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# Simple rigid body system
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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read_data data.rigid
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velocity all create 100.0 4928459
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# 2 chains of connected bodies
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group clump1 id <> 1 9
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group clump2 id <> 9 18
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group clump3 id <> 18 27
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group clump4 id <> 27 36
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group clump5 id <> 37 45
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group clump6 id <> 45 54
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group clump7 id <> 54 63
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group clump8 id <> 63 72
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group clump9 id <> 72 81
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fix 1 all poems file connected-bodies2.dat
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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#dump 1 all atom 50 dump.rigid.poems
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#dump 2 all image 100 image.*.jpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 100 movie.mpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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timestep 0.0001
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thermo 50
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run 10000
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328
examples/rigid/log.20Mar22.rigid.poems.g++.1
Normal file
328
examples/rigid/log.20Mar22.rigid.poems.g++.1
Normal file
@ -0,0 +1,328 @@
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LAMMPS (17 Feb 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# Simple rigid body system
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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read_data data.rigid
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Reading data file ...
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orthogonal box = (-12 -12 -12) to (12 12 12)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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81 atoms
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read_data CPU = 0.000 seconds
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velocity all create 100.0 4928459
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# 1 chain of connected bodies
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group clump1 id <> 1 9
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9 atoms in group clump1
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group clump2 id <> 9 18
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10 atoms in group clump2
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group clump3 id <> 18 27
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10 atoms in group clump3
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group clump4 id <> 27 36
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10 atoms in group clump4
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group clump5 id <> 36 45
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10 atoms in group clump5
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group clump6 id <> 45 54
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10 atoms in group clump6
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group clump7 id <> 54 63
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10 atoms in group clump7
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group clump8 id <> 63 72
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10 atoms in group clump8
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group clump9 id <> 72 81
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10 atoms in group clump9
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fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
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1 clusters, 9 bodies, 8 joints, 81 atoms
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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#dump 1 all atom 50 dump.rigid.poems
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#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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timestep 0.0001
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thermo 50
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run 10000
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|
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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|
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Your simulation uses code contributions which should be cited:
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- fix poems command:
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@Article{Mukherjee08,
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author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
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title = {Substructured molecular dynamics using multibody dynamics algorithms},
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journal = {Intl.~J.~Non-linear Mechanics},
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year = 2008,
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volume = 43,
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pages = {1045--1055}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
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|
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 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 = 18 18 18
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
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Step Temp E_pair E_mol TotEng Press
|
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0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045742
|
||||
850 17821.483 711.53827 0 3681.7854 7.438428
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19374 0 3681.3037 11.787982
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184716
|
||||
1150 20849.582 206.01696 0 3680.9472 -0.86699118
|
||||
1200 21815.003 45.317409 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064083
|
||||
1300 20780.781 217.36511 0 3680.8286 6.0538604
|
||||
1350 20558.971 254.36489 0 3680.8601 -3.6773868
|
||||
1400 21485.029 99.812844 0 3680.6511 -16.185479
|
||||
1450 21771.107 52.159653 0 3680.6775 -2.4756655
|
||||
1500 21520.949 93.503876 0 3680.3286 2.1023573
|
||||
1550 21351.419 121.6813 0 3680.2511 5.5159876
|
||||
1600 20778.804 216.92191 0 3680.0559 15.089203
|
||||
1650 21477.636 100.21873 0 3679.8247 -1.1045277
|
||||
1700 18501.33 596.4807 0 3680.0357 -15.6798
|
||||
1750 18563.64 587.34824 0 3681.2882 33.532308
|
||||
1800 19110.175 494.82517 0 3679.8543 18.024074
|
||||
1850 21364.178 119.23765 0 3679.9339 2.5290144
|
||||
1900 20146.588 322.15509 0 3679.9197 5.7317299
|
||||
1950 20692.676 231.25264 0 3680.0319 4.297803
|
||||
2000 20943.902 189.11251 0 3679.7629 -22.643824
|
||||
2050 19667.823 401.86882 0 3679.8394 3.6241915
|
||||
2100 20280.125 299.81485 0 3679.8357 7.4804047
|
||||
2150 19181.201 483.6306 0 3680.4975 22.63342
|
||||
2200 21301.144 130.54014 0 3680.7308 4.7074288
|
||||
2250 20484.876 266.98315 0 3681.1291 -8.6578278
|
||||
2300 18648.161 573.07329 0 3681.1001 -5.2550954
|
||||
2350 21515.748 95.243054 0 3681.201 -9.386512
|
||||
2400 21462.551 104.18267 0 3681.2745 -29.46442
|
||||
2450 20107.732 330.99437 0 3682.2831 35.38497
|
||||
2500 20771.509 220.47713 0 3682.3953 -12.324858
|
||||
2550 20499.887 265.58494 0 3682.2327 -22.713874
|
||||
2600 21462.182 105.24427 0 3682.2747 -10.175788
|
||||
2650 21004.949 181.51383 0 3682.3387 4.949195
|
||||
2700 18673.552 570.45017 0 3682.7089 21.201437
|
||||
2750 21257.562 139.198 0 3682.1249 -7.5793039
|
||||
2800 21559.645 88.844759 0 3682.119 -6.2360467
|
||||
2850 20865.227 204.46262 0 3682.0004 0.39575069
|
||||
2900 19428.614 443.93293 0 3682.0352 12.796676
|
||||
2950 19630.1 410.18487 0 3681.8681 -0.50572623
|
||||
3000 19663.218 404.06316 0 3681.2661 6.0827093
|
||||
3050 19087.572 500.8452 0 3682.1073 -6.3526476
|
||||
3100 18229.94 643.77681 0 3682.1001 11.453637
|
||||
3150 18927.492 527.51919 0 3682.1011 -1.662863
|
||||
3200 18320.514 628.55895 0 3681.978 21.176126
|
||||
3250 18204.677 647.96462 0 3682.0775 11.331521
|
||||
3300 19231.978 477.02117 0 3682.3509 3.8381593
|
||||
3350 18153.44 656.70376 0 3682.2772 15.135615
|
||||
3400 17476.768 770.0598 0 3682.8545 -3.394312
|
||||
3450 21097.531 166.17241 0 3682.4276 3.74301
|
||||
3500 17605.784 747.54808 0 3681.8454 3.3420627
|
||||
3550 19238.34 476.00608 0 3682.3961 1.1413836
|
||||
3600 18155.288 656.57434 0 3682.4557 3.4360446
|
||||
3650 18735.622 559.2377 0 3681.8413 28.760363
|
||||
3700 15310.261 1134.4215 0 3686.1317 44.207018
|
||||
3750 15377.116 1123.4786 0 3686.3313 7.6773215
|
||||
3800 18798.895 549.05928 0 3682.2084 -12.905825
|
||||
3850 18322.563 628.87744 0 3682.6379 -16.067793
|
||||
3900 19963.049 355.65441 0 3682.8292 3.4694064
|
||||
3950 19925.48 361.2507 0 3682.1641 5.0058567
|
||||
4000 19141.423 492.41081 0 3682.648 -12.782769
|
||||
4050 20022.241 345.61655 0 3682.6568 -3.0149905
|
||||
4100 21348.635 124.95646 0 3683.0624 -4.85779
|
||||
4150 21011.812 181.1132 0 3683.0819 -3.9526196
|
||||
4200 20222.276 312.63945 0 3683.0187 -23.63437
|
||||
4250 20957.757 189.77152 0 3682.731 -1.3712469
|
||||
4300 20070.215 337.5751 0 3682.611 -6.8816517
|
||||
4350 21322.437 129.09228 0 3682.8318 -6.9442178
|
||||
4400 19440.445 442.77531 0 3682.8495 -0.11606236
|
||||
4450 20964.516 188.67174 0 3682.7577 4.8533525
|
||||
4500 13530.08 1428.5497 0 3683.563 12.333187
|
||||
4550 20461.637 272.58882 0 3682.8616 4.5111943
|
||||
4600 17072.994 836.58228 0 3682.0812 5.7611617
|
||||
4650 18860.748 539.82027 0 3683.2782 -2.5558958
|
||||
4700 18373.927 621.04093 0 3683.3621 5.4020702
|
||||
4750 20321.437 296.63662 0 3683.5428 8.9571617
|
||||
4800 21083.122 169.84086 0 3683.6946 10.566368
|
||||
4850 20499.669 267.7012 0 3684.3128 4.2924237
|
||||
4900 20308.781 300.38168 0 3685.1785 -12.396923
|
||||
4950 21043.303 178.56295 0 3685.7801 3.8923762
|
||||
5000 20718.383 232.52208 0 3685.5859 -12.43234
|
||||
5050 21005.749 184.4363 0 3685.3945 -7.6463487
|
||||
5100 20714.133 233.27745 0 3685.6329 -1.6944135
|
||||
5150 19577.452 422.73035 0 3685.639 -21.831219
|
||||
5200 14044.647 1343.9545 0 3684.729 -6.8407194
|
||||
5250 19089.805 504.0893 0 3685.7235 4.05641
|
||||
5300 21094.745 169.94699 0 3685.7378 -0.66593212
|
||||
5350 19907.559 366.77598 0 3684.7024 1.5248525
|
||||
5400 20382.81 289.13263 0 3686.2676 -11.919321
|
||||
5450 19593.693 420.70548 0 3686.3209 -1.1568628
|
||||
5500 20906.08 202.09801 0 3686.4447 -2.4284971
|
||||
5550 16315.465 965.56973 0 3684.8138 -33.178221
|
||||
5600 19714.57 400.39687 0 3686.1586 19.950231
|
||||
5650 20561.724 259.54797 0 3686.502 8.2074524
|
||||
5700 19349.502 460.7789 0 3685.6959 16.252649
|
||||
5750 21006.818 185.56805 0 3686.7044 -11.96089
|
||||
5800 20268.2 307.97547 0 3686.0089 17.322311
|
||||
5850 21018.322 184.16179 0 3687.2154 -14.379909
|
||||
5900 19695.647 404.57094 0 3687.1787 -20.718904
|
||||
5950 21021.687 183.66311 0 3687.2776 -15.206081
|
||||
6000 18947.535 529.30554 0 3687.2281 17.863927
|
||||
6050 15272.373 1141.012 0 3686.4075 -0.43375666
|
||||
6100 17766.197 721.75792 0 3682.7908 11.378913
|
||||
6150 18612.573 584.06688 0 3686.1623 17.543241
|
||||
6200 19005.155 518.97146 0 3686.4973 -16.223107
|
||||
6250 20997.507 187.55499 0 3687.1394 -11.613546
|
||||
6300 19639.901 413.58048 0 3686.8974 14.407136
|
||||
6350 19580.399 423.02818 0 3686.428 -5.5801796
|
||||
6400 14134.119 1332.0662 0 3687.7527 84.864425
|
||||
6450 21598.824 87.419966 0 3687.224 -5.8358352
|
||||
6500 18208.216 649.29108 0 3683.9938 -8.1510884
|
||||
6550 19364.586 459.59813 0 3687.0291 -12.053563
|
||||
6600 20710.927 235.11914 0 3686.9403 -1.0470193
|
||||
6650 21132.334 165.08091 0 3687.1366 1.0785471
|
||||
6700 20217.285 317.589 0 3687.1365 0.055447462
|
||||
6750 21232.279 148.57412 0 3687.2873 -2.4551657
|
||||
6800 20292.683 304.76539 0 3686.8793 -0.42311295
|
||||
6850 19056.291 510.49927 0 3686.5478 6.9533826
|
||||
6900 20429.82 282.23764 0 3687.2076 -4.2360112
|
||||
6950 21281.278 140.27361 0 3687.1533 -0.07475261
|
||||
7000 17173.388 824.54446 0 3686.7758 10.753828
|
||||
7050 18079.7 674.56274 0 3687.846 12.975804
|
||||
7100 16433.233 950.73904 0 3689.6112 -10.5102
|
||||
7150 19033.335 515.59672 0 3687.8193 0.29109447
|
||||
7200 17286.428 809.02352 0 3690.0948 2.3015698
|
||||
7250 16811.962 886.6645 0 3688.6582 -7.4787512
|
||||
7300 15992.461 1023.4849 0 3688.895 -5.2354222
|
||||
7350 19211.451 487.63129 0 3689.5398 8.4351737
|
||||
7400 19065.682 511.95629 0 3689.57 -12.47448
|
||||
7450 21369.265 128.10098 0 3689.6451 2.2930546
|
||||
7500 16807.109 888.64602 0 3689.8308 14.761969
|
||||
7550 18063.046 679.21873 0 3689.7264 3.8950434
|
||||
7600 17794.987 724.55404 0 3690.3851 14.379016
|
||||
7650 17904.751 706.14354 0 3690.2688 23.813776
|
||||
7700 19670.09 411.3021 0 3689.6504 14.099245
|
||||
7750 18082.562 675.23975 0 3689.0001 15.788521
|
||||
7800 17776.135 726.91445 0 3689.6037 6.9780735
|
||||
7850 17062.575 846.33412 0 3690.0966 -8.9289256
|
||||
7900 19059.2 513.07737 0 3689.6107 16.992843
|
||||
7950 16269.685 978.48914 0 3690.1033 11.180179
|
||||
8000 20115.278 336.91405 0 3689.4604 -6.4882518
|
||||
8050 21173.72 161.15229 0 3690.1056 -2.2164491
|
||||
8100 19238.235 484.42784 0 3690.8004 23.412709
|
||||
8150 18438.4 617.58743 0 3690.6542 0.89156316
|
||||
8200 21438.764 117.12721 0 3690.2546 -1.7193227
|
||||
8250 21195.806 157.66607 0 3690.3003 3.820447
|
||||
8300 21177.549 161.13702 0 3690.7286 0.94938203
|
||||
8350 21060.267 181.06887 0 3691.1135 2.8179025
|
||||
8400 20087.113 343.46206 0 3691.3142 8.1484473
|
||||
8450 19298.478 474.87133 0 3691.2843 -16.239664
|
||||
8500 21654.353 82.083485 0 3691.1423 -8.1464138
|
||||
8550 19920.544 371.34795 0 3691.4386 20.765144
|
||||
8600 21692.293 75.655154 0 3691.0373 -13.316763
|
||||
8650 21231.322 151.8989 0 3690.4526 -11.388238
|
||||
8700 19530.647 434.89585 0 3690.0037 2.7433786
|
||||
8750 19720.63 403.07773 0 3689.8493 -6.416414
|
||||
8800 21321.378 136.04091 0 3689.604 1.3661635
|
||||
8850 19811.906 387.80489 0 3689.7893 3.704143
|
||||
8900 19734.167 400.92444 0 3689.9523 2.5685155
|
||||
8950 21076.459 177.18119 0 3689.9244 -11.939513
|
||||
9000 20967.246 195.42966 0 3689.9707 2.0092705
|
||||
9050 21122.023 169.62103 0 3689.9582 2.3791301
|
||||
9100 20169.346 328.27229 0 3689.8299 -3.5017988
|
||||
9150 21418.641 119.84513 0 3689.6187 2.486073
|
||||
9200 20876.042 210.26452 0 3689.6048 -5.3839897
|
||||
9250 21572.38 93.74407 0 3689.1407 -8.3676952
|
||||
9300 20944.78 197.98577 0 3688.7824 1.3278314
|
||||
9350 20706.52 237.48767 0 3688.5744 4.6944204
|
||||
9400 16412.314 953.47251 0 3688.8581 26.134976
|
||||
9450 20461.68 277.76243 0 3688.0424 17.647445
|
||||
9500 20893.994 205.64261 0 3687.9749 -10.642418
|
||||
9550 20503.447 270.63504 0 3687.8761 -17.769897
|
||||
9600 19677.799 408.05887 0 3687.692 -2.7938604
|
||||
9650 17480.971 774.1855 0 3687.6806 0.59827043
|
||||
9700 17799.126 721.50817 0 3688.0292 44.387928
|
||||
9750 20443.384 280.16837 0 3687.399 3.0619324
|
||||
9800 20545.255 263.40108 0 3687.6102 3.6229381
|
||||
9850 20722.819 233.57142 0 3687.3745 0.86462694
|
||||
9900 21128.462 165.09767 0 3686.508 -6.9636843
|
||||
9950 21343.307 130.46714 0 3687.685 -9.7382705
|
||||
10000 20623.887 250.37866 0 3687.6932 2.7529835
|
||||
Loop time of 2.27157 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 38035.351 tau/day, 4402.240 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.092926 | 0.092926 | 0.092926 | 0.0 | 4.09
|
||||
Neigh | 0.076362 | 0.076362 | 0.076362 | 0.0 | 3.36
|
||||
Comm | 0.0069691 | 0.0069691 | 0.0069691 | 0.0 | 0.31
|
||||
Output | 0.0037444 | 0.0037444 | 0.0037444 | 0.0 | 0.16
|
||||
Modify | 2.0832 | 2.0832 | 2.0832 | 0.0 | 91.71
|
||||
Other | | 0.00841 | | | 0.37
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 62 ave 62 max 62 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 905 ave 905 max 905 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 905
|
||||
Ave neighs/atom = 11.17284
|
||||
Neighbor list builds = 991
|
||||
Dangerous builds = 927
|
||||
Total wall time: 0:00:02
|
||||
328
examples/rigid/log.20Mar22.rigid.poems.g++.4
Normal file
328
examples/rigid/log.20Mar22.rigid.poems.g++.4
Normal file
@ -0,0 +1,328 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix poems command:
|
||||
|
||||
@Article{Mukherjee08,
|
||||
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
|
||||
title = {Substructured molecular dynamics using multibody dynamics algorithms},
|
||||
journal = {Intl.~J.~Non-linear Mechanics},
|
||||
year = 2008,
|
||||
volume = 43,
|
||||
pages = {1045--1055}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045742
|
||||
850 17821.483 711.53827 0 3681.7854 7.4384281
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19374 0 3681.3037 11.787982
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184716
|
||||
1150 20849.582 206.01696 0 3680.9472 -0.86699115
|
||||
1200 21815.003 45.317409 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064083
|
||||
1300 20780.781 217.36511 0 3680.8286 6.0538606
|
||||
1350 20558.971 254.36489 0 3680.8601 -3.6773868
|
||||
1400 21485.03 99.812843 0 3680.6511 -16.185479
|
||||
1450 21771.107 52.159652 0 3680.6775 -2.4756656
|
||||
1500 21520.949 93.503872 0 3680.3286 2.1023574
|
||||
1550 21351.419 121.68131 0 3680.2511 5.5159875
|
||||
1600 20778.804 216.92191 0 3680.0559 15.089203
|
||||
1650 21477.636 100.21877 0 3679.8247 -1.104524
|
||||
1700 18501.329 596.48084 0 3680.0357 -15.679806
|
||||
1750 18563.639 587.34841 0 3681.2882 33.532316
|
||||
1800 19110.174 494.82524 0 3679.8543 18.024079
|
||||
1850 21364.178 119.23767 0 3679.9339 2.5290075
|
||||
1900 20146.588 322.15506 0 3679.9197 5.7317368
|
||||
1950 20692.674 231.25288 0 3680.0319 4.2977982
|
||||
2000 20943.904 189.11229 0 3679.7629 -22.643749
|
||||
2050 19667.815 401.87016 0 3679.8394 3.6240972
|
||||
2100 20280.109 299.81759 0 3679.8357 7.4803647
|
||||
2150 19181.146 483.63975 0 3680.4974 22.634167
|
||||
2200 21301.194 130.53171 0 3680.7308 4.7072523
|
||||
2250 20484.79 266.99736 0 3681.1291 -8.6583002
|
||||
2300 18648.002 573.09962 0 3681.1 -5.2548835
|
||||
2350 21515.851 95.225745 0 3681.2009 -9.3875216
|
||||
2400 21462.37 104.21272 0 3681.2744 -29.459857
|
||||
2450 20108.034 330.94394 0 3682.2829 35.37058
|
||||
2500 20771.818 220.42545 0 3682.3951 -12.318936
|
||||
2550 20502.815 265.09577 0 3682.2316 -22.726822
|
||||
2600 21462.006 105.2733 0 3682.2744 -10.180394
|
||||
2650 21009.656 180.72738 0 3682.3367 4.9580828
|
||||
2700 18680.012 569.37179 0 3682.7071 21.114114
|
||||
2750 21256.19 139.42201 0 3682.1203 -7.4744399
|
||||
2800 21552.267 90.071446 0 3682.1159 -6.2906304
|
||||
2850 20879.958 202.00905 0 3682.0021 0.57990903
|
||||
2900 19018.645 512.35214 0 3682.1262 13.883084
|
||||
2950 19819.365 378.55747 0 3681.785 -0.7348943
|
||||
3000 20269.229 303.35149 0 3681.5563 6.3088075
|
||||
3050 19236.727 475.99457 0 3682.1158 -10.703575
|
||||
3100 18391.55 616.96976 0 3682.2281 9.850079
|
||||
3150 20258.563 305.82076 0 3682.248 7.1951283
|
||||
3200 20716.384 229.15502 0 3681.8856 2.9042294
|
||||
3250 18662.237 572.0784 0 3682.4512 9.2108597
|
||||
3300 19162.278 488.60646 0 3682.3195 3.3306562
|
||||
3350 21235.679 142.98279 0 3682.2626 0.29397483
|
||||
3400 17677.053 736.09247 0 3682.2679 32.75269
|
||||
3450 20852.392 206.65618 0 3682.0548 -4.8319056
|
||||
3500 21182.918 151.46754 0 3681.9539 -5.6330382
|
||||
3550 20589.85 250.40724 0 3682.049 12.582133
|
||||
3600 20973.659 186.28043 0 3681.8903 10.935266
|
||||
3650 17838.632 707.92145 0 3681.0268 -17.200926
|
||||
3700 21538.002 92.744409 0 3682.4114 -0.72124229
|
||||
3750 21390.294 117.90865 0 3682.9576 -7.8431786
|
||||
3800 17921.046 696.50311 0 3683.344 -9.4641531
|
||||
3850 20356.471 290.22624 0 3682.9715 2.4593463
|
||||
3900 20374.077 287.10249 0 3682.782 -1.9519082
|
||||
3950 20563.915 255.29993 0 3682.619 -6.124649
|
||||
4000 20991.467 184.76183 0 3683.3397 1.8954961
|
||||
4050 17805.623 716.24698 0 3683.8509 -20.454944
|
||||
4100 19916.389 363.86301 0 3683.2611 -0.27912557
|
||||
4150 19221.623 480.01232 0 3683.6161 -11.562492
|
||||
4200 20526.82 261.78571 0 3682.9224 -3.9522917
|
||||
4250 20922.813 196.1799 0 3683.3154 0.11947446
|
||||
4300 19956.66 357.78133 0 3683.8914 19.156093
|
||||
4350 19735.73 394.45981 0 3683.7482 14.865775
|
||||
4400 21702.656 67.099805 0 3684.2092 -13.502538
|
||||
4450 18163.055 656.97231 0 3684.1482 -0.6243111
|
||||
4500 17477.718 771.25976 0 3684.2127 -0.4664004
|
||||
4550 20676.507 238.19814 0 3684.2827 -19.444969
|
||||
4600 17322.922 796.77058 0 3683.9242 27.003966
|
||||
4650 11905.158 1704.9151 0 3689.1082 15.574169
|
||||
4700 18689.079 569.80982 0 3684.6563 -14.67311
|
||||
4750 19821.745 381.01914 0 3684.6433 5.0436795
|
||||
4800 20621.335 247.96269 0 3684.8518 -16.407263
|
||||
4850 21923.814 30.965964 0 3684.935 -13.418244
|
||||
4900 18840.555 544.41538 0 3684.5079 11.005357
|
||||
4950 15366.601 1124.2481 0 3685.3482 17.412375
|
||||
5000 18274.314 639.01311 0 3684.732 5.3261109
|
||||
5050 21173.687 155.83673 0 3684.7845 5.4056809
|
||||
5100 21738.219 61.75201 0 3684.7885 -2.631945
|
||||
5150 16597.949 918.84841 0 3685.1732 -10.124101
|
||||
5200 20752.758 225.95919 0 3684.7522 -5.2441372
|
||||
5250 17652.088 741.2645 0 3683.2793 2.0080739
|
||||
5300 19907.523 366.53115 0 3684.4516 8.4266792
|
||||
5350 20104.189 334.14522 0 3684.8433 17.21925
|
||||
5400 21499.848 101.71631 0 3685.0243 -6.1103541
|
||||
5450 21203.533 151.14574 0 3685.068 -5.9468503
|
||||
5500 21076.513 172.45652 0 3685.2088 5.1418181
|
||||
5550 20158.398 325.56609 0 3685.2992 -1.6486034
|
||||
5600 20787.836 221.19563 0 3685.835 -10.66805
|
||||
5650 19687.154 404.77204 0 3685.9644 -23.49128
|
||||
5700 20419.311 282.58328 0 3685.8017 -0.52808211
|
||||
5750 19738.522 395.95893 0 3685.7126 1.3889817
|
||||
5800 18300.025 635.66905 0 3685.6732 23.490447
|
||||
5850 20585.004 255.02032 0 3685.8543 -0.20699939
|
||||
5900 20373.839 290.15881 0 3685.7987 -7.9712187
|
||||
5950 18163.832 659.91192 0 3687.2173 5.4494586
|
||||
6000 21049.247 177.43029 0 3685.6382 2.9138342
|
||||
6050 21239.803 145.77613 0 3685.7433 -1.4927769
|
||||
6100 20686.361 237.86454 0 3685.5913 -0.95516297
|
||||
6150 20461.754 275.31546 0 3685.6079 -3.4166412
|
||||
6200 19264.208 474.73017 0 3685.4316 11.750757
|
||||
6250 21180.813 155.31746 0 3685.4529 2.8188219
|
||||
6300 21047.543 177.4394 0 3685.3632 1.8641486
|
||||
6350 20232.576 313.17716 0 3685.2731 2.8150209
|
||||
6400 20185.616 321.33454 0 3685.6038 -3.8697311
|
||||
6450 18969.632 523.95865 0 3685.5639 0.6725512
|
||||
6500 17592.574 753.49959 0 3685.5952 -1.2557393
|
||||
6550 21279.049 138.42524 0 3684.9335 -1.208945
|
||||
6600 21408.457 116.4143 0 3684.4904 -1.5332953
|
||||
6650 19758.218 391.17316 0 3684.2096 1.8511312
|
||||
6700 20766.943 223.44631 0 3684.6036 -2.3672623
|
||||
6750 20399.631 284.09914 0 3684.0377 -5.4089876
|
||||
6800 21296.628 135.14662 0 3684.5847 -3.8442549
|
||||
6850 20641.481 244.4451 0 3684.692 1.4020639
|
||||
6900 20852.81 209.23009 0 3684.6984 1.8512104
|
||||
6950 20940.555 194.66882 0 3684.7614 -6.554676
|
||||
7000 19496.988 435.28199 0 3684.78 -15.120269
|
||||
7050 19796.829 385.04227 0 3684.5138 -4.1068804
|
||||
7100 19945.264 360.42431 0 3684.635 -4.0629042
|
||||
7150 19431.123 446.12911 0 3684.6497 -6.8321751
|
||||
7200 16864.851 873.80043 0 3684.6089 14.309069
|
||||
7250 20438.75 277.85982 0 3684.3181 -11.41223
|
||||
7300 17688.684 734.01576 0 3682.1298 35.938373
|
||||
7350 21573.419 88.63421 0 3684.204 -3.9032749
|
||||
7400 21198.486 150.72249 0 3683.8034 -7.1477117
|
||||
7450 20586.708 252.93928 0 3684.0572 -7.6634645
|
||||
7500 21815.377 48.180377 0 3684.0765 0.97457507
|
||||
7550 17791.352 718.87564 0 3684.101 28.248235
|
||||
7600 21828.874 45.928597 0 3684.0742 -0.25814944
|
||||
7650 20827.961 212.35674 0 3683.6835 -3.4083384
|
||||
7700 21319.176 130.43547 0 3683.6315 -12.434856
|
||||
7750 20127.904 328.69643 0 3683.3471 -16.975711
|
||||
7800 21741.772 59.679206 0 3683.3078 3.6261863
|
||||
7850 19612.334 414.37418 0 3683.0964 1.3763274
|
||||
7900 20071.318 337.74624 0 3682.9658 -0.40982763
|
||||
7950 17925.664 695.29582 0 3682.9065 17.104439
|
||||
8000 19125.978 492.76383 0 3680.4268 10.807662
|
||||
8050 20233.848 310.42681 0 3682.7347 13.386237
|
||||
8100 20551.619 257.86699 0 3683.1368 -13.97515
|
||||
8150 21578.323 86.88362 0 3683.2708 -9.6811587
|
||||
8200 21154.833 157.72897 0 3683.5344 0.62312375
|
||||
8250 21321.143 129.83967 0 3683.3636 1.9536438
|
||||
8300 21041.696 176.04177 0 3682.9911 4.7475567
|
||||
8350 19883.39 369.32649 0 3683.2247 -7.0959328
|
||||
8400 21626.067 79.062992 0 3683.4075 -14.919059
|
||||
8450 21375.201 120.86836 0 3683.4019 -5.3461514
|
||||
8500 20281.059 303.10304 0 3683.2796 3.7975093
|
||||
8550 21170.533 154.48432 0 3682.9065 -1.1568561
|
||||
8600 17754.931 724.00158 0 3683.1568 14.15254
|
||||
8650 20685.478 235.65879 0 3683.2385 -5.2694179
|
||||
8700 21489.165 101.90509 0 3683.4326 -4.2510612
|
||||
8750 21106.682 165.41638 0 3683.1968 -3.9186708
|
||||
8800 19149.516 491.5843 0 3683.1702 -11.419849
|
||||
8850 21451.865 108.1814 0 3683.4923 -7.8256219
|
||||
8900 19567.4 421.81206 0 3683.0454 -0.71997056
|
||||
8950 20934.097 194.48033 0 3683.4965 -7.0106879
|
||||
9000 18531.559 595.25957 0 3683.8528 3.7449399
|
||||
9050 18868.821 537.22549 0 3682.029 9.9926092
|
||||
9100 19972.527 354.73119 0 3683.4858 -0.30871263
|
||||
9150 19641.651 409.18618 0 3682.7947 -1.3036238
|
||||
9200 20019.08 346.19657 0 3682.7099 6.7425386
|
||||
9250 19259.286 473.04973 0 3682.9308 -24.120659
|
||||
9300 21597.757 82.971857 0 3682.598 -13.748483
|
||||
9350 19348.379 457.23576 0 3681.9656 3.1571402
|
||||
9400 19129.588 493.35235 0 3681.617 8.6293783
|
||||
9450 20337.025 291.20959 0 3680.7138 6.8590795
|
||||
9500 20581.788 249.65891 0 3679.9569 -18.892836
|
||||
9550 19482.069 433.0077 0 3680.0192 23.029778
|
||||
9600 19182.794 482.96871 0 3680.101 -11.081731
|
||||
9650 20086.771 332.5311 0 3680.3263 -18.939681
|
||||
9700 20274.046 300.98818 0 3679.9959 6.7538762
|
||||
9750 18743.595 555.08045 0 3679.0129 8.2757138
|
||||
9800 19464.311 435.66288 0 3679.7148 7.0528759
|
||||
9850 21249.848 138.27382 0 3679.9152 -10.847402
|
||||
9900 21156.214 153.84621 0 3679.8819 -7.8359674
|
||||
9950 21643.134 72.547515 0 3679.7365 -10.507744
|
||||
10000 19587.948 414.64942 0 3679.3075 6.1173553
|
||||
Loop time of 2.36879 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 36474.344 tau/day, 4221.568 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.005348 | 0.024925 | 0.056071 | 12.2 | 1.05
|
||||
Neigh | 0.0075012 | 0.022046 | 0.043933 | 9.3 | 0.93
|
||||
Comm | 0.13135 | 0.16461 | 0.1917 | 5.9 | 6.95
|
||||
Output | 0.0036298 | 0.004271 | 0.0056384 | 1.2 | 0.18
|
||||
Modify | 2.1147 | 2.1322 | 2.1418 | 0.7 | 90.01
|
||||
Other | | 0.02072 | | | 0.87
|
||||
|
||||
Nlocal: 20.25 ave 81 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 41 ave 78 max 11 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 193.5 ave 774 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 774
|
||||
Ave neighs/atom = 9.5555556
|
||||
Neighbor list builds = 989
|
||||
Dangerous builds = 915
|
||||
Total wall time: 0:00:02
|
||||
330
examples/rigid/log.20Mar22.rigid.poems2.g++.1
Normal file
330
examples/rigid/log.20Mar22.rigid.poems2.g++.1
Normal file
@ -0,0 +1,330 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
2 clusters, 9 bodies, 7 joints, 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems2
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix poems command:
|
||||
|
||||
@Article{Mukherjee08,
|
||||
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
|
||||
title = {Substructured molecular dynamics using multibody dynamics algorithms},
|
||||
journal = {Intl.~J.~Non-linear Mechanics},
|
||||
year = 2008,
|
||||
volume = 43,
|
||||
pages = {1045--1055}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -2.7403788
|
||||
50 12774.759 1538.7382 0 3904.4344 18.086359
|
||||
100 19803.641 237.21132 0 3904.5523 -3.1528278
|
||||
150 20259.6 152.62072 0 3904.3985 -4.6173524
|
||||
200 20705.978 69.977442 0 3904.4178 9.0928158
|
||||
250 19552.211 283.50525 0 3904.285 15.670465
|
||||
300 19266.324 333.5792 0 3901.4169 7.2119197
|
||||
350 20738.325 63.738945 0 3904.1694 -23.03999
|
||||
400 20616.682 86.082444 0 3903.9864 -13.783584
|
||||
450 19831.326 230.13858 0 3902.6063 0.42074361
|
||||
500 20365.825 131.47231 0 3902.9213 0.6921524
|
||||
550 20794.102 52.163238 0 3902.9229 4.5895354
|
||||
600 20853.873 40.899172 0 3902.7275 2.3593042
|
||||
650 19255.802 336.29509 0 3902.1844 10.341742
|
||||
700 18526.969 471.02462 0 3901.9448 -0.61898691
|
||||
750 18960.662 391.26068 0 3902.4944 12.04731
|
||||
800 20142.432 172.05177 0 3902.1317 4.6838621
|
||||
850 19932.48 210.71175 0 3901.9118 3.4716043
|
||||
900 20243.528 153.13972 0 3901.9411 3.6490762
|
||||
950 20388.132 126.88722 0 3902.4671 -4.4518463
|
||||
1000 20076.333 184.61915 0 3902.4586 -2.272315
|
||||
1050 20859.506 39.696993 0 3902.5684 6.45166
|
||||
1100 15284.661 1072.1908 0 3902.6836 21.194042
|
||||
1150 19658.317 261.99809 0 3902.4272 -2.874422
|
||||
1200 20767.681 56.717094 0 3902.5839 -34.817444
|
||||
1250 20625.583 82.586399 0 3902.1388 11.697329
|
||||
1300 20690.013 71.006478 0 3902.4903 -29.292777
|
||||
1350 20936.019 26.022786 0 3903.0634 1.0316025
|
||||
1400 19753.559 244.81785 0 3902.8844 6.7138514
|
||||
1450 15690.149 998.342 0 3903.9252 48.124557
|
||||
1500 20234.455 155.92516 0 3903.0465 13.17221
|
||||
1550 20779.631 55.063009 0 3903.1428 -2.639045
|
||||
1600 20642.753 80.233905 0 3902.9659 -2.4688467
|
||||
1650 18785.696 423.90402 0 3902.7365 -5.6466663
|
||||
1700 20965.076 20.760444 0 3903.182 -0.45364296
|
||||
1750 18935.406 396.96067 0 3903.5173 25.913302
|
||||
1800 20581.559 91.756972 0 3903.1567 3.8217234
|
||||
1850 20616.946 85.184849 0 3903.1378 4.1907972
|
||||
1900 16602.053 828.40949 0 3902.8637 -0.49505122
|
||||
1950 20175.526 166.53362 0 3902.7421 5.603825
|
||||
2000 20261.924 150.39322 0 3902.6014 -1.196958
|
||||
2050 20170.339 167.40504 0 3902.6531 -0.80849882
|
||||
2100 19820.132 231.26755 0 3901.6624 3.1476607
|
||||
2150 20666.19 75.838461 0 3902.9106 0.53899287
|
||||
2200 19873.51 222.53286 0 3902.8124 7.9310276
|
||||
2250 18548.063 467.69698 0 3902.5235 16.905356
|
||||
2300 20616.61 84.762399 0 3902.6531 -6.7872951
|
||||
2350 18167.738 538.13635 0 3902.5322 -11.458285
|
||||
2400 20120.227 177.01954 0 3902.9875 -1.2593018
|
||||
2450 20436.599 118.32469 0 3902.8801 -6.5989174
|
||||
2500 18919.923 400.26361 0 3903.9531 32.37476
|
||||
2550 19675.809 259.77151 0 3903.4398 19.437327
|
||||
2600 19739.842 247.86388 0 3903.3901 -7.519784
|
||||
2650 20557.026 96.530313 0 3903.387 0.60211646
|
||||
2700 20666.602 76.099892 0 3903.2484 0.16825503
|
||||
2750 20924.585 28.453883 0 3903.3771 2.4227171
|
||||
2800 20360.659 132.8596 0 3903.352 4.1440877
|
||||
2850 20783.475 54.518625 0 3903.3102 -0.57312067
|
||||
2900 20456.181 115.03745 0 3903.2191 -20.118887
|
||||
2950 20779.493 55.321394 0 3903.3756 -0.26783079
|
||||
3000 20011.867 197.30216 0 3903.2035 -1.4704201
|
||||
3050 20741.875 62.208723 0 3903.2966 -7.5432815
|
||||
3100 21001.754 14.148298 0 3903.362 2.9676438
|
||||
3150 20244.086 154.44639 0 3903.3512 -1.9071213
|
||||
3200 20639.615 81.136426 0 3903.2873 1.4826467
|
||||
3250 20735.244 63.529571 0 3903.3895 2.1127055
|
||||
3300 20142.891 173.22282 0 3903.3878 4.7739415
|
||||
3350 19963.765 206.21899 0 3903.2126 5.5410771
|
||||
3400 16628.667 824.13627 0 3903.519 36.087673
|
||||
3450 19228.218 342.81569 0 3903.5968 3.1057274
|
||||
3500 19759.293 244.57876 0 3903.707 2.2339557
|
||||
3550 19853.21 227.06362 0 3903.584 -1.0882119
|
||||
3600 19673.516 260.64854 0 3903.8923 -10.63775
|
||||
3650 19619.238 270.5393 0 3903.7316 -6.3746003
|
||||
3700 20756.865 59.790243 0 3903.6542 -8.3015766
|
||||
3750 20265.025 150.47347 0 3903.2559 -5.7284695
|
||||
3800 20944.683 24.669276 0 3903.3142 -0.070552298
|
||||
3850 19344.831 320.59492 0 3902.971 13.040749
|
||||
3900 19978.209 203.00247 0 3902.6708 0.15638133
|
||||
3950 19864.118 224.19359 0 3902.734 0.453229
|
||||
4000 17606.216 642.71493 0 3903.1252 -12.656002
|
||||
4050 18017.895 566.54102 0 3903.1883 12.133906
|
||||
4100 20092.963 182.17593 0 3903.095 7.7445947
|
||||
4150 20555.337 96.395074 0 3902.939 -6.5429752
|
||||
4200 20709.781 67.869199 0 3903.0138 -2.8653003
|
||||
4250 18956.203 392.20748 0 3902.6155 -1.6249728
|
||||
4300 17816.204 603.72704 0 3903.0241 23.089239
|
||||
4350 18979.742 388.04678 0 3902.8138 3.2511108
|
||||
4400 20272.085 148.82367 0 3902.9135 1.9518268
|
||||
4450 18820.003 417.74789 0 3902.9337 6.3979299
|
||||
4500 19991.936 200.50131 0 3902.7117 3.5118553
|
||||
4550 20915.092 29.663898 0 3902.8291 -2.3174641
|
||||
4600 20690.37 71.125087 0 3902.6752 -12.008575
|
||||
4650 18893.76 404.50849 0 3903.3529 15.006184
|
||||
4700 18611.123 456.1263 0 3902.6306 -5.3574892
|
||||
4750 20497.821 106.5856 0 3902.4784 0.85039837
|
||||
4800 20803.214 50.120522 0 3902.5675 3.8610873
|
||||
4850 18849.598 411.72635 0 3902.3927 9.2029058
|
||||
4900 18121.714 546.68042 0 3902.5533 9.4522272
|
||||
4950 20377.499 128.99323 0 3902.6041 5.3825395
|
||||
5000 20686.114 72.039749 0 3902.8016 -5.706271
|
||||
5050 20180.449 165.51368 0 3902.634 -16.418461
|
||||
5100 20274.947 148.36657 0 3902.9864 -5.6668309
|
||||
5150 18042.324 560.74137 0 3901.9125 3.6791541
|
||||
5200 20794.666 52.204446 0 3903.0685 -1.4517721
|
||||
5250 19073.55 371.18834 0 3903.3272 -13.457439
|
||||
5300 20821.412 47.364313 0 3903.1813 2.258098
|
||||
5350 20583.073 91.271191 0 3902.9513 5.4323985
|
||||
5400 20490.967 108.41184 0 3903.0353 4.122905
|
||||
5450 18141.79 543.66874 0 3903.2594 -0.19951075
|
||||
5500 20274.012 148.55528 0 3903.002 5.0489974
|
||||
5550 17806.237 605.43454 0 3902.8858 43.80619
|
||||
5600 20999.825 14.341937 0 3903.1983 1.0879933
|
||||
5650 20930.929 27.025347 0 3903.1234 -7.0860209
|
||||
5700 20677.725 73.853093 0 3903.0614 2.6864775
|
||||
5750 20521.264 102.87509 0 3903.1092 2.6940548
|
||||
5800 20792.571 52.596021 0 3903.0721 1.2910217
|
||||
5850 20518.674 103.26595 0 3903.0204 -9.2547271
|
||||
5900 18417.885 491.66696 0 3902.3865 -12.049357
|
||||
5950 17243.837 709.37858 0 3902.6817 -6.2357188
|
||||
6000 20262.525 149.56918 0 3901.8885 -0.28964823
|
||||
6050 19883.554 219.14043 0 3901.2801 2.3071707
|
||||
6100 16548.178 838.47869 0 3902.956 -11.715644
|
||||
6150 19601.177 272.14674 0 3901.9944 -0.9008056
|
||||
6200 20499.796 106.2363 0 3902.4949 0.79071424
|
||||
6250 19601.106 272.50139 0 3902.3359 -1.9306693
|
||||
6300 17210.685 712.70535 0 3899.8692 4.8890923
|
||||
6350 19911.896 214.91041 0 3902.2985 12.691129
|
||||
6400 18834.642 411.87123 0 3899.7678 -1.9447856
|
||||
6450 20216.311 158.39781 0 3902.1591 2.6009109
|
||||
6500 20452.025 114.97122 0 3902.3832 0.14644416
|
||||
6550 19142.589 357.34097 0 3902.2649 2.8968485
|
||||
6600 20412.915 122.08784 0 3902.2573 3.1343105
|
||||
6650 17317.867 699.39994 0 3906.4123 42.25563
|
||||
6700 20479.771 109.8036 0 3902.3537 1.3520625
|
||||
6750 20306.902 142.12484 0 3902.6623 2.2032106
|
||||
6800 20755.367 58.994834 0 3902.5814 -0.90518094
|
||||
6850 20471.259 111.7197 0 3902.6936 1.5799331
|
||||
6900 20702.025 69.15032 0 3902.8586 9.3910371
|
||||
6950 20477.695 110.34414 0 3902.5099 1.8181164
|
||||
7000 20560.727 95.057704 0 3902.5998 -15.686006
|
||||
7050 20336.675 136.39386 0 3902.4448 1.3704327
|
||||
7100 20757.399 58.950153 0 3902.913 -6.4250981
|
||||
7150 20870.958 38.095649 0 3903.088 -4.1962169
|
||||
7200 20706.869 68.489134 0 3903.0944 2.8322659
|
||||
7250 20386.713 127.7432 0 3903.0604 6.0287391
|
||||
7300 18391.773 497.21001 0 3903.0939 19.202343
|
||||
7350 20178.898 166.4993 0 3903.3322 1.5682417
|
||||
7400 16858.704 781.78682 0 3903.7691 21.317514
|
||||
7450 17509.513 660.71963 0 3903.2221 -5.9456143
|
||||
7500 19974.601 204.20412 0 3903.2043 -0.69202711
|
||||
7550 20917.053 29.73415 0 3903.2626 -3.9962577
|
||||
7600 20923.518 28.482703 0 3903.2083 -1.9016251
|
||||
7650 20549.528 97.630612 0 3903.0987 3.5512257
|
||||
7700 20861.441 39.903885 0 3903.1337 2.4426264
|
||||
7750 18843.349 413.64461 0 3903.1537 2.677739
|
||||
7800 20616.054 85.214364 0 3903.0021 3.9639004
|
||||
7850 16478.851 851.93376 0 3903.5728 7.3763128
|
||||
7900 20312.115 141.35103 0 3902.8539 4.6707271
|
||||
7950 20389.623 127.16589 0 3903.0219 3.4414001
|
||||
8000 20452.117 115.30715 0 3902.7362 -1.0162528
|
||||
8050 20857.093 40.791886 0 3903.2164 -15.150068
|
||||
8100 19817.543 233.4997 0 3903.415 0.89346046
|
||||
8150 18649.521 449.9112 0 3903.5262 -0.40053588
|
||||
8200 19619.276 270.37616 0 3903.5754 5.5161492
|
||||
8250 20393.176 127.01336 0 3903.5275 2.122613
|
||||
8300 19145.912 358.00424 0 3903.5435 3.863924
|
||||
8350 19636.311 267.17226 0 3903.5262 -7.1496084
|
||||
8400 19086.332 368.86693 0 3903.3729 7.0968952
|
||||
8450 19494.416 292.89527 0 3902.9723 3.1750935
|
||||
8500 20041.919 191.77756 0 3903.244 0.95215503
|
||||
8550 20357.561 133.15478 0 3903.0736 -0.14020152
|
||||
8600 16998.797 756.07003 0 3903.9954 -16.724408
|
||||
8650 20853.26 41.386996 0 3903.1017 -3.2612965
|
||||
8700 20767.768 57.360884 0 3903.2438 1.1157649
|
||||
8750 20752.546 60.106518 0 3903.1705 0.39130547
|
||||
8800 20574.407 92.99798 0 3903.0734 0.61728166
|
||||
8850 20326.99 138.94203 0 3903.1995 -1.9434522
|
||||
8900 17408.108 679.53222 0 3903.2559 21.935371
|
||||
8950 20471.21 112.2721 0 3903.2368 1.8142747
|
||||
9000 19129.591 360.35257 0 3902.8694 4.5786395
|
||||
9050 20439.668 117.89541 0 3903.0191 2.5585685
|
||||
9100 20780.375 54.788664 0 3903.0062 3.8312459
|
||||
9150 19904.559 216.61504 0 3902.6445 12.150414
|
||||
9200 20961.295 21.52065 0 3903.2419 -0.2120699
|
||||
9250 19315.252 326.44175 0 3903.3402 -19.740867
|
||||
9300 20653.002 78.77764 0 3903.4076 -7.8068233
|
||||
9350 18961.572 391.20947 0 3902.6117 -12.660843
|
||||
9400 16262.179 892.67633 0 3904.191 22.2435
|
||||
9450 17064.394 743.33301 0 3903.406 36.139436
|
||||
9500 18075.588 555.06436 0 3902.3954 24.598176
|
||||
9550 20487.738 109.06287 0 3903.0884 2.6320759
|
||||
9600 20358.609 133.36993 0 3903.4828 0.76449113
|
||||
9650 19849.022 228.46312 0 3904.208 9.5547064
|
||||
9700 20448.112 116.8757 0 3903.5632 -1.0845697
|
||||
9750 20472.78 112.51661 0 3903.7722 -0.30676738
|
||||
9800 19491.99 293.35361 0 3902.9814 -20.10857
|
||||
9850 19895.603 218.42479 0 3902.7957 -0.18235641
|
||||
9900 19704.336 254.55068 0 3903.5019 14.553184
|
||||
9950 17689.462 627.9788 0 3903.805 4.9918088
|
||||
10000 20184.205 165.29396 0 3903.1097 2.9472364
|
||||
Loop time of 2.2898 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 37732.583 tau/day, 4367.197 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.053341 | 0.053341 | 0.053341 | 0.0 | 2.33
|
||||
Neigh | 0.056174 | 0.056174 | 0.056174 | 0.0 | 2.45
|
||||
Comm | 0.0087028 | 0.0087028 | 0.0087028 | 0.0 | 0.38
|
||||
Output | 0.0036774 | 0.0036774 | 0.0036774 | 0.0 | 0.16
|
||||
Modify | 2.1598 | 2.1598 | 2.1598 | 0.0 | 94.32
|
||||
Other | | 0.008128 | | | 0.35
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 113 ave 113 max 113 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 582 ave 582 max 582 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 582
|
||||
Ave neighs/atom = 7.1851852
|
||||
Neighbor list builds = 993
|
||||
Dangerous builds = 950
|
||||
Total wall time: 0:00:02
|
||||
330
examples/rigid/log.20Mar22.rigid.poems2.g++.4
Normal file
330
examples/rigid/log.20Mar22.rigid.poems2.g++.4
Normal file
@ -0,0 +1,330 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
2 clusters, 9 bodies, 7 joints, 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems2
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix poems command:
|
||||
|
||||
@Article{Mukherjee08,
|
||||
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
|
||||
title = {Substructured molecular dynamics using multibody dynamics algorithms},
|
||||
journal = {Intl.~J.~Non-linear Mechanics},
|
||||
year = 2008,
|
||||
volume = 43,
|
||||
pages = {1045--1055}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -2.7403788
|
||||
50 12774.759 1538.7382 0 3904.4344 18.086358
|
||||
100 19803.641 237.21132 0 3904.5523 -3.1528278
|
||||
150 20259.6 152.62072 0 3904.3985 -4.6173524
|
||||
200 20705.978 69.977039 0 3904.4174 9.0928122
|
||||
250 19552.211 283.50525 0 3904.285 15.670466
|
||||
300 19266.324 333.5792 0 3901.4169 7.2119197
|
||||
350 20738.325 63.738945 0 3904.1694 -23.03999
|
||||
400 20616.682 86.082444 0 3903.9864 -13.783584
|
||||
450 19831.326 230.13858 0 3902.6063 0.42074361
|
||||
500 20365.825 131.47271 0 3902.9217 0.69215592
|
||||
550 20794.102 52.163238 0 3902.9229 4.5895354
|
||||
600 20853.873 40.899172 0 3902.7275 2.3593042
|
||||
650 19255.802 336.29509 0 3902.1844 10.341742
|
||||
700 18526.969 471.02462 0 3901.9448 -0.61898691
|
||||
750 18960.662 391.26068 0 3902.4944 12.04731
|
||||
800 20142.432 172.05197 0 3902.1319 4.6838632
|
||||
850 19932.48 210.71175 0 3901.9118 3.4716031
|
||||
900 20243.528 153.13972 0 3901.9411 3.6490762
|
||||
950 20388.132 126.88722 0 3902.4671 -4.4518463
|
||||
1000 20076.333 184.61915 0 3902.4586 -2.272315
|
||||
1050 20859.506 39.696993 0 3902.5684 6.45166
|
||||
1100 15284.661 1072.1908 0 3902.6836 21.194042
|
||||
1150 19658.317 261.99809 0 3902.4272 -2.8744219
|
||||
1200 20767.681 56.717095 0 3902.5839 -34.817444
|
||||
1250 20625.583 82.586198 0 3902.1386 11.697328
|
||||
1300 20690.013 71.006478 0 3902.4903 -29.29278
|
||||
1350 20936.019 26.022786 0 3903.0634 1.0316025
|
||||
1400 19753.56 244.81784 0 3902.8844 6.7138497
|
||||
1450 15690.149 998.34213 0 3903.9252 48.124569
|
||||
1500 20234.455 155.92516 0 3903.0465 13.172207
|
||||
1550 20779.631 55.063019 0 3903.1428 -2.6390455
|
||||
1600 20642.753 80.233821 0 3902.9659 -2.4688431
|
||||
1650 18785.698 423.90364 0 3902.7365 -5.6466892
|
||||
1700 20965.076 20.760451 0 3903.182 -0.45366172
|
||||
1750 18935.412 396.95958 0 3903.5173 25.913174
|
||||
1800 20581.554 91.757912 0 3903.1567 3.8218442
|
||||
1850 20616.949 85.184789 0 3903.1382 4.1907933
|
||||
1900 16601.896 828.43849 0 3902.8638 -0.49468175
|
||||
1950 20175.564 166.52646 0 3902.7421 5.6035728
|
||||
2000 20262.525 150.28224 0 3902.6017 -1.1967705
|
||||
2050 20168.994 167.65314 0 3902.6521 -0.80723928
|
||||
2100 19810.955 232.96524 0 3901.6605 3.1936531
|
||||
2150 20667.232 75.645145 0 3902.9103 0.54812734
|
||||
2200 19863.772 224.34646 0 3902.8228 7.9294465
|
||||
2250 18808.943 419.2084 0 3902.3461 14.344526
|
||||
2300 20573.665 92.761842 0 3902.6999 -6.7671703
|
||||
2350 19075.104 369.95414 0 3902.3809 -9.5353568
|
||||
2400 20273.873 148.53775 0 3902.9586 -1.93796
|
||||
2450 20087.769 182.30216 0 3902.2593 2.131796
|
||||
2500 20711.602 67.530554 0 3903.0124 2.6280244
|
||||
2550 19971.224 204.75926 0 3903.134 3.1760522
|
||||
2600 20620.084 85.027145 0 3903.5612 -0.92888063
|
||||
2650 19737.546 248.65474 0 3903.7559 -3.3218688
|
||||
2700 20650.724 79.522243 0 3903.7303 -7.5918025
|
||||
2750 19863.245 225.2505 0 3903.6292 9.2140221
|
||||
2800 18992.457 386.73547 0 3903.8572 2.6244537
|
||||
2850 18703.899 440.48356 0 3904.1685 14.561348
|
||||
2900 17939.805 581.74599 0 3903.932 -8.0863089
|
||||
2950 20867.516 39.38186 0 3903.7367 3.0985423
|
||||
3000 19767.994 242.8847 0 3903.6243 1.5943109
|
||||
3050 20397.448 126.31591 0 3903.6212 -0.14982775
|
||||
3100 20978.114 19.126395 0 3903.9623 -9.6797253
|
||||
3150 18303.556 513.8514 0 3903.3989 4.5940322
|
||||
3200 19156.505 356.46608 0 3903.9671 10.071308
|
||||
3250 17484.205 666.52199 0 3904.3377 -4.1641768
|
||||
3300 18069.94 557.75947 0 3904.0447 11.868707
|
||||
3350 20855.645 41.964632 0 3904.1212 5.4186293
|
||||
3400 18011.986 568.76255 0 3904.3155 25.262783
|
||||
3450 18669.69 446.92755 0 3904.2776 -4.194499
|
||||
3500 20248.799 154.22147 0 3903.9991 3.9211572
|
||||
3550 20226.024 158.64726 0 3904.2072 1.5299114
|
||||
3600 20267.02 151.25631 0 3904.4082 -8.9821729
|
||||
3650 20522.946 103.65382 0 3904.1994 -14.433796
|
||||
3700 20892.319 35.294614 0 3904.2426 -21.264596
|
||||
3750 19942.202 211.02993 0 3904.0304 -1.6428817
|
||||
3800 20421.678 122.08118 0 3903.8734 1.7137935
|
||||
3850 17899.53 588.82593 0 3903.5536 -24.450276
|
||||
3900 20721.119 66.486999 0 3903.7312 -7.1772088
|
||||
3950 20946.484 24.799445 0 3903.778 -0.4028037
|
||||
4000 20985.362 17.608355 0 3903.7865 4.7522266
|
||||
4050 19969.779 205.46466 0 3903.5719 18.941639
|
||||
4100 20479.578 110.56561 0 3903.08 2.3715952
|
||||
4150 18110.701 549.53348 0 3903.367 1.133321
|
||||
4200 19321.098 325.58216 0 3903.5634 -3.7574942
|
||||
4250 20734.436 63.87616 0 3903.5865 0.48350623
|
||||
4300 19446.823 302.1727 0 3903.4362 4.0462392
|
||||
4350 20494.669 108.1918 0 3903.501 2.9789077
|
||||
4400 20379.244 129.61413 0 3903.5482 4.0881089
|
||||
4450 19710.564 253.4251 0 3903.5295 5.3334683
|
||||
4500 20744.753 61.785082 0 3903.406 4.0015409
|
||||
4550 19948.024 208.76984 0 3902.8484 2.705423
|
||||
4600 18367.368 502.69569 0 3904.0602 21.476471
|
||||
4650 20559.367 96.133242 0 3903.4234 2.2549454
|
||||
4700 20940.135 25.547808 0 3903.3505 -8.9042666
|
||||
4750 20128.703 175.82088 0 3903.3584 -8.1450176
|
||||
4800 20632.27 82.543887 0 3903.3347 -0.55649542
|
||||
4850 19864.539 224.63792 0 3903.2563 7.1553461
|
||||
4900 19332.037 323.15561 0 3903.1625 17.020214
|
||||
4950 19055.575 373.68069 0 3902.4908 10.149457
|
||||
5000 20219.484 159.21383 0 3903.5627 3.1806346
|
||||
5050 17557.761 652.32864 0 3903.7659 10.733736
|
||||
5100 20615.337 85.795304 0 3903.4503 -3.6035636
|
||||
5150 20759.853 59.155843 0 3903.573 2.0152286
|
||||
5200 20082.007 184.39375 0 3903.2839 -5.3745109
|
||||
5250 18689.521 442.59842 0 3903.6208 -9.8911164
|
||||
5300 20038.496 192.34221 0 3903.1749 -2.1437039
|
||||
5350 19897.455 218.70142 0 3903.4154 0.64582116
|
||||
5400 18732.385 434.21543 0 3903.1755 12.98676
|
||||
5450 19831.487 230.79099 0 3903.2886 11.439958
|
||||
5500 20079.89 184.6953 0 3903.1935 4.0906279
|
||||
5550 20453.497 115.47128 0 3903.1559 7.8844436
|
||||
5600 16673.041 815.52661 0 3903.1267 -20.17797
|
||||
5650 19691.378 256.6412 0 3903.1928 3.7103317
|
||||
5700 20345.743 135.29997 0 3903.0302 5.6373816
|
||||
5750 20769.613 56.906603 0 3903.1312 -17.564762
|
||||
5800 20713.369 67.38314 0 3903.1922 -5.340631
|
||||
5850 20799.947 51.348865 0 3903.1909 -2.7827653
|
||||
5900 19581.933 273.51588 0 3899.7997 12.347375
|
||||
5950 20444.438 116.909 0 3902.9161 -0.74896654
|
||||
6000 18970.948 389.99664 0 3903.1352 26.642912
|
||||
6050 19414.753 307.13217 0 3902.4568 25.86316
|
||||
6100 20780.042 54.586474 0 3902.7424 1.5387425
|
||||
6150 20885.872 35.091585 0 3902.8456 -8.251884
|
||||
6200 19825.81 231.40943 0 3902.8558 6.7196589
|
||||
6250 20578.278 92.255994 0 3903.0481 -5.9647091
|
||||
6300 20093.43 181.8699 0 3902.8754 -9.9906069
|
||||
6350 20605.294 87.180289 0 3902.9755 -3.5643876
|
||||
6400 19737.257 247.84828 0 3902.8958 -4.2783347
|
||||
6450 19884.717 220.81633 0 3903.1714 3.8758905
|
||||
6500 18719.372 436.94802 0 3903.4984 1.7865904
|
||||
6550 20096.883 181.63346 0 3903.2784 2.395512
|
||||
6600 20888.673 35.003062 0 3903.2758 2.7728947
|
||||
6650 20437.85 118.16373 0 3902.9507 8.1456757
|
||||
6700 19241.051 339.73065 0 3902.8882 13.740454
|
||||
6750 20407.542 123.94326 0 3903.1177 7.6285942
|
||||
6800 20536.785 99.976706 0 3903.0851 8.3496632
|
||||
6850 20625.328 83.579677 0 3903.0849 6.5074992
|
||||
6900 20705.37 68.944625 0 3903.2724 3.1905177
|
||||
6950 18872.424 408.67134 0 3903.5647 6.2638845
|
||||
7000 20072.762 186.18051 0 3903.3586 -22.780407
|
||||
7050 20461.879 114.07495 0 3903.3117 -11.495523
|
||||
7100 19811.566 234.50237 0 3903.3108 1.1212695
|
||||
7150 20742.918 61.884088 0 3903.1651 -3.7907508
|
||||
7200 20911.192 30.599903 0 3903.0429 -7.0262304
|
||||
7250 20879.755 36.30274 0 3902.9241 -5.8018787
|
||||
7300 20682.32 72.703261 0 3902.7626 -3.3446789
|
||||
7350 19401.046 309.70672 0 3902.493 3.4836528
|
||||
7400 20220.542 157.83897 0 3902.3838 2.3400031
|
||||
7450 17691.193 625.47764 0 3901.6244 25.239568
|
||||
7500 19745.294 245.02566 0 3901.5615 5.3622843
|
||||
7550 19685.719 256.70983 0 3902.2133 3.4560563
|
||||
7600 18830.192 415.10021 0 3902.1727 -0.10282681
|
||||
7650 19613.136 270.18979 0 3902.2521 8.2241536
|
||||
7700 20989.015 15.636879 0 3902.4915 1.2955204
|
||||
7750 20301.583 142.90625 0 3902.4586 0.12548373
|
||||
7800 18360.147 502.50342 0 3902.5307 17.117272
|
||||
7850 20796.478 51.032537 0 3902.2321 -3.0993883
|
||||
7900 20284.267 145.64296 0 3901.9887 -1.2682383
|
||||
7950 20280.983 146.13471 0 3901.8723 3.5999841
|
||||
8000 20915.869 28.730821 0 3902.0399 2.4987291
|
||||
8050 20745.162 60.19981 0 3901.8964 4.0643481
|
||||
8100 20509.039 103.70462 0 3901.6748 1.0771863
|
||||
8150 20212.97 158.64893 0 3901.7916 3.0000215
|
||||
8200 20323.463 138.25912 0 3901.8634 -1.2802945
|
||||
8250 19997.284 198.37183 0 3901.5727 -2.6431964
|
||||
8300 20138.402 171.75824 0 3901.092 1.7669897
|
||||
8350 20367.568 130.22531 0 3901.9972 -1.2153731
|
||||
8400 19945.534 208.35675 0 3901.9741 1.6021151
|
||||
8450 20112.534 177.18642 0 3901.7298 2.2413008
|
||||
8500 20686.7 71.116816 0 3901.9873 2.2888545
|
||||
8550 18081.94 553.83586 0 3902.3432 7.8257937
|
||||
8600 18320.081 505.67086 0 3898.2784 16.554878
|
||||
8650 20235.305 154.43021 0 3901.709 3.1740823
|
||||
8700 20355.413 132.22512 0 3901.746 4.3436482
|
||||
8750 20087.188 182.11349 0 3901.9631 10.422134
|
||||
8800 20400.795 124.09819 0 3902.0232 2.1179177
|
||||
8850 20678.731 72.825797 0 3902.2204 -3.4491441
|
||||
8900 20372.643 129.5072 0 3902.2189 -8.2166415
|
||||
8950 20851.731 40.899364 0 3902.331 -5.8382839
|
||||
9000 20318.076 139.61775 0 3902.2243 -4.1960802
|
||||
9050 16879.415 776.53739 0 3902.3549 -14.429475
|
||||
9100 19135.149 358.68223 0 3902.2284 -15.50479
|
||||
9150 20689.556 70.939656 0 3902.339 -2.9876179
|
||||
9200 19949.801 207.54882 0 3901.9564 6.4259245
|
||||
9250 20207.027 160.2813 0 3902.3233 1.7402195
|
||||
9300 20030.005 192.99466 0 3902.2548 5.300728
|
||||
9350 19795.291 236.24003 0 3902.0347 5.8677745
|
||||
9400 18232.093 526.18752 0 3902.501 19.344893
|
||||
9450 18789.641 422.30568 0 3901.8687 -7.5185247
|
||||
9500 16332.599 874.10423 0 3898.6597 16.241378
|
||||
9550 18572.572 462.19972 0 3901.5649 -10.777359
|
||||
9600 19859.645 223.32209 0 3901.0341 0.89631957
|
||||
9650 19092.741 365.35768 0 3901.0504 6.7830005
|
||||
9700 18391.154 495.72792 0 3901.4972 6.0683847
|
||||
9750 17790.092 608.60997 0 3903.0714 8.2090184
|
||||
9800 17681.783 628.99951 0 3903.4038 14.231747
|
||||
9850 17804.412 605.54067 0 3902.654 22.308453
|
||||
9900 19134.472 359.37911 0 3902.7999 8.5633158
|
||||
9950 20099.055 180.28604 0 3902.3332 4.7905855
|
||||
10000 20035.447 192.30744 0 3902.5754 1.8299201
|
||||
Loop time of 2.31994 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 37242.315 tau/day, 4310.453 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0052789 | 0.014781 | 0.038634 | 11.4 | 0.64
|
||||
Neigh | 0.0081228 | 0.016514 | 0.033404 | 7.7 | 0.71
|
||||
Comm | 0.12269 | 0.13668 | 0.14951 | 3.1 | 5.89
|
||||
Output | 0.0034489 | 0.0039413 | 0.0050811 | 1.1 | 0.17
|
||||
Modify | 2.1036 | 2.1312 | 2.1509 | 1.2 | 91.86
|
||||
Other | | 0.01685 | | | 0.73
|
||||
|
||||
Nlocal: 20.25 ave 36 max 0 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 35.25 ave 47 max 24 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 137.5 ave 252 max 0 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 550
|
||||
Ave neighs/atom = 6.7901235
|
||||
Neighbor list builds = 994
|
||||
Dangerous builds = 956
|
||||
Total wall time: 0:00:02
|
||||
329
examples/rigid/log.20Mar22.rigid.poems3.g++.1
Normal file
329
examples/rigid/log.20Mar22.rigid.poems3.g++.1
Normal file
@ -0,0 +1,329 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all poems file unconnected-bodies.dat
|
||||
WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035)
|
||||
9 clusters, 9 bodies, 0 joints, 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix poems command:
|
||||
|
||||
@Article{Mukherjee08,
|
||||
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
|
||||
title = {Substructured molecular dynamics using multibody dynamics algorithms},
|
||||
journal = {Intl.~J.~Non-linear Mechanics},
|
||||
year = 2008,
|
||||
volume = 43,
|
||||
pages = {1045--1055}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.686 571.71596 0 5265.8207 32.006226
|
||||
100 16298.5 136.65142 0 5267.6607 16.443791
|
||||
150 16682.639 17.488068 0 5269.43 14.900278
|
||||
200 16733.955 1.3724268 0 5269.4692 14.569123
|
||||
250 16738.877 -0.15250573 0 5269.4939 14.496287
|
||||
300 16738.611 -0.05516662 0 5269.5077 14.495909
|
||||
350 16738.515 -0.01744351 0 5269.5152 14.496329
|
||||
400 16738.488 -0.0060096677 0 5269.5178 14.496497
|
||||
450 16738.479 -0.0012712918 0 5269.5199 14.496575
|
||||
500 16738.479 -0.00081070354 0 5269.5203 14.49658
|
||||
550 16738.479 -0.00083205205 0 5269.5203 14.496577
|
||||
600 16738.479 -0.0005835658 0 5269.5206 14.49658
|
||||
650 16738.479 -0.00047227225 0 5269.5206 14.496583
|
||||
700 16738.479 0 0 5269.521 14.496593
|
||||
750 16738.479 0 0 5269.5211 14.496595
|
||||
800 16738.479 0 0 5269.5211 14.496596
|
||||
850 16738.479 0 0 5269.5211 14.496595
|
||||
900 16738.479 0 0 5269.5212 14.496593
|
||||
950 16738.485 -0.003532391 0 5269.5196 14.496546
|
||||
1000 16738.609 -0.051135033 0 5269.5109 14.496098
|
||||
1050 16737.381 0.32991002 0 5269.5055 14.525627
|
||||
1100 16737.915 0.16210932 0 5269.5058 14.531848
|
||||
1150 16738.726 -0.089235332 0 5269.5098 14.509768
|
||||
1200 16738.49 -0.0075446298 0 5269.5169 14.510489
|
||||
1250 16738.48 0 0 5269.5214 14.510585
|
||||
1300 16738.48 0 0 5269.5214 14.510587
|
||||
1350 16738.48 0 0 5269.5215 14.510588
|
||||
1400 16738.48 -0.00044742303 0 5269.5211 14.510581
|
||||
1450 16738.481 -0.0010975104 0 5269.5207 14.51057
|
||||
1500 16738.481 -0.00057925965 0 5269.5211 14.510575
|
||||
1550 16738.48 0 0 5269.5216 14.510582
|
||||
1600 16738.48 0 0 5269.5216 14.510581
|
||||
1650 16738.481 0 0 5269.5216 14.510581
|
||||
1700 16738.481 0 0 5269.5217 14.510582
|
||||
1750 16738.481 0 0 5269.5217 14.510583
|
||||
1800 16738.481 0 0 5269.5217 14.510585
|
||||
1850 16738.481 0 0 5269.5218 14.510585
|
||||
1900 16738.481 0 0 5269.5218 14.510585
|
||||
1950 16738.487 -0.0031700155 0 5269.5206 14.510534
|
||||
2000 16738.514 -0.013238802 0 5269.5188 14.510401
|
||||
2050 16738.578 -0.03654435 0 5269.5158 14.510155
|
||||
2100 16738.656 -0.063182323 0 5269.5137 14.510082
|
||||
2150 16738.63 -0.056004395 0 5269.5127 14.510096
|
||||
2200 16738.579 -0.038415873 0 5269.5143 14.510273
|
||||
2250 16738.538 -0.023709094 0 5269.516 14.510414
|
||||
2300 16738.512 -0.013252539 0 5269.5182 14.510501
|
||||
2350 16738.491 -0.0045593284 0 5269.5203 14.510598
|
||||
2400 16738.482 -0.00052242487 0 5269.5217 14.510655
|
||||
2450 16738.486 -0.0023245722 0 5269.5211 14.510627
|
||||
2500 16738.491 -0.005189304 0 5269.5197 14.510606
|
||||
2550 16738.604 -0.044988104 0 5269.5155 14.510185
|
||||
2600 16738.446 0.00096754005 0 5269.5117 14.510521
|
||||
2650 16732.887 1.753125 0 5269.5138 14.598792
|
||||
2700 16738.784 -0.10629556 0 5269.5107 14.499176
|
||||
2750 16734.136 1.359459 0 5269.5135 14.594678
|
||||
2800 16738.608 -0.047184149 0 5269.5147 14.510254
|
||||
2850 16738.509 -0.012527238 0 5269.5181 14.509344
|
||||
2900 16738.487 -0.0026065529 0 5269.521 14.509512
|
||||
2950 16738.498 -0.0082248532 0 5269.519 14.509457
|
||||
3000 16738.683 -0.071294028 0 5269.514 14.509005
|
||||
3050 16717.444 6.5874862 0 5269.4864 14.834144
|
||||
3100 16657.654 25.431253 0 5269.5074 14.467824
|
||||
3150 16739.322 -0.28964062 0 5269.497 13.658821
|
||||
3200 16733.615 1.4969789 0 5269.487 11.998304
|
||||
3250 16737.289 0.35071214 0 5269.4974 11.918931
|
||||
3300 16732.493 1.8663821 0 5269.503 12.109003
|
||||
3350 16738.717 -0.087719164 0 5269.5085 11.979747
|
||||
3400 16738.586 -0.045267897 0 5269.5095 11.97972
|
||||
3450 16738.662 -0.071274216 0 5269.5076 11.979564
|
||||
3500 16738.853 -0.13644992 0 5269.5026 11.979658
|
||||
3550 16729.612 2.7475277 0 5269.4774 12.195939
|
||||
3600 16728.659 3.0596069 0 5269.4893 12.241248
|
||||
3650 16738.923 -0.15949792 0 5269.5014 11.991857
|
||||
3700 16738.76 -0.10695054 0 5269.5028 11.992932
|
||||
3750 16738.751 -0.10105954 0 5269.5057 11.993137
|
||||
3800 16738.597 -0.048627545 0 5269.5097 11.993456
|
||||
3850 16738.507 -0.016053927 0 5269.5138 11.992973
|
||||
3900 16738.485 -0.0060825487 0 5269.5169 11.993052
|
||||
3950 16738.475 -0.0014953722 0 5269.5183 11.993119
|
||||
4000 16738.472 -0.00054315391 0 5269.5184 11.99315
|
||||
4050 16738.472 -0.00023792127 0 5269.5187 11.993172
|
||||
4100 16738.472 0 0 5269.5189 11.993188
|
||||
4150 16738.472 0 0 5269.5189 11.993188
|
||||
4200 16738.472 0 0 5269.519 11.993178
|
||||
4250 16738.472 0 0 5269.519 11.993164
|
||||
4300 16738.472 0 0 5269.5191 11.993152
|
||||
4350 16738.473 0 0 5269.5191 11.993147
|
||||
4400 16738.473 0 0 5269.5192 11.993149
|
||||
4450 16738.473 0 0 5269.5192 11.993158
|
||||
4500 16738.473 0 0 5269.5193 11.99317
|
||||
4550 16738.473 0 0 5269.5193 11.993176
|
||||
4600 16738.473 0 0 5269.5194 11.993174
|
||||
4650 16738.473 0 0 5269.5194 11.993167
|
||||
4700 16738.474 0 0 5269.5195 11.993162
|
||||
4750 16738.474 0 0 5269.5195 11.99316
|
||||
4800 16738.474 0 0 5269.5196 11.99316
|
||||
4850 16738.474 0 0 5269.5196 11.993163
|
||||
4900 16738.474 0 0 5269.5197 11.99317
|
||||
4950 16738.474 0 0 5269.5197 11.993176
|
||||
5000 16738.475 0 0 5269.5198 11.993174
|
||||
5050 16738.475 0 0 5269.5198 11.993165
|
||||
5100 16738.475 0 0 5269.5199 11.993155
|
||||
5150 16738.475 0 0 5269.5199 11.99315
|
||||
5200 16738.475 0 0 5269.52 11.993153
|
||||
5250 16738.475 0 0 5269.52 11.993161
|
||||
5300 16738.476 0 0 5269.5201 11.993173
|
||||
5350 16738.476 0 0 5269.5201 11.993185
|
||||
5400 16738.476 0 0 5269.5202 11.993189
|
||||
5450 16738.476 0 0 5269.5202 11.993181
|
||||
5500 16738.476 0 0 5269.5203 11.993165
|
||||
5550 16738.483 -0.0030091905 0 5269.5195 11.993097
|
||||
5600 16738.534 -0.020777802 0 5269.5177 11.992799
|
||||
5650 16738.649 -0.059321662 0 5269.5153 11.993266
|
||||
5700 16409.08 103.75288 0 5269.5745 23.626238
|
||||
5750 16738.578 -0.036776519 0 5269.5155 11.910545
|
||||
5800 16738.484 -0.0047306177 0 5269.518 11.911008
|
||||
5850 16738.477 -0.00022082692 0 5269.5202 11.911078
|
||||
5900 16738.477 -0.00033136078 0 5269.5203 11.91107
|
||||
5950 16738.478 -0.00036902212 0 5269.5203 11.911052
|
||||
6000 16738.477 0 0 5269.5206 11.911044
|
||||
6050 16738.477 0 0 5269.5207 11.911034
|
||||
6100 16738.478 0 0 5269.5207 11.911032
|
||||
6150 16738.478 0 0 5269.5208 11.911037
|
||||
6200 16738.478 0 0 5269.5208 11.911049
|
||||
6250 16738.478 0 0 5269.5209 11.911062
|
||||
6300 16738.478 0 0 5269.5209 11.911068
|
||||
6350 16738.478 0 0 5269.521 11.911065
|
||||
6400 16738.478 0 0 5269.521 11.911058
|
||||
6450 16738.479 0 0 5269.5211 11.911052
|
||||
6500 16738.479 0 0 5269.5211 11.911047
|
||||
6550 16738.479 0 0 5269.5212 11.911046
|
||||
6600 16738.479 0 0 5269.5212 11.911049
|
||||
6650 16738.479 0 0 5269.5213 11.911056
|
||||
6700 16738.479 0 0 5269.5213 11.911062
|
||||
6750 16738.48 0 0 5269.5214 11.91106
|
||||
6800 16738.48 0 0 5269.5214 11.911051
|
||||
6850 16738.48 0 0 5269.5215 11.911044
|
||||
6900 16738.48 0 0 5269.5215 11.911041
|
||||
6950 16738.48 0 0 5269.5216 11.911045
|
||||
7000 16738.48 0 0 5269.5216 11.911053
|
||||
7050 16738.481 0 0 5269.5217 11.911063
|
||||
7100 16738.481 0 0 5269.5217 11.911071
|
||||
7150 16738.481 0 0 5269.5218 11.911072
|
||||
7200 16738.481 0 0 5269.5218 11.911063
|
||||
7250 16738.481 0 0 5269.5219 11.911048
|
||||
7300 16738.481 0 0 5269.5219 11.911036
|
||||
7350 16738.482 0 0 5269.522 11.911031
|
||||
7400 16738.482 0 0 5269.522 11.911035
|
||||
7450 16738.482 0 0 5269.5221 11.911046
|
||||
7500 16738.482 0 0 5269.5221 11.911062
|
||||
7550 16738.482 0 0 5269.5222 11.911077
|
||||
7600 16738.482 0 0 5269.5222 11.911081
|
||||
7650 16738.483 0 0 5269.5223 11.911071
|
||||
7700 16738.483 0 0 5269.5223 11.911054
|
||||
7750 16738.483 0 0 5269.5224 11.911039
|
||||
7800 16738.483 0 0 5269.5224 11.911031
|
||||
7850 16738.483 0 0 5269.5225 11.911031
|
||||
7900 16738.483 0 0 5269.5226 11.911039
|
||||
7950 16738.484 0 0 5269.5226 11.911052
|
||||
8000 16738.484 0 0 5269.5227 11.911065
|
||||
8050 16738.484 0 0 5269.5227 11.91107
|
||||
8100 16738.484 0 0 5269.5228 11.911065
|
||||
8150 16738.484 0 0 5269.5228 11.911056
|
||||
8200 16738.484 0 0 5269.5229 11.911047
|
||||
8250 16738.485 0 0 5269.5229 11.911042
|
||||
8300 16738.485 0 0 5269.523 11.911041
|
||||
8350 16738.485 0 0 5269.523 11.911046
|
||||
8400 16738.485 0 0 5269.5231 11.911055
|
||||
8450 16738.485 0 0 5269.5231 11.911062
|
||||
8500 16738.485 0 0 5269.5232 11.91106
|
||||
8550 16738.486 0 0 5269.5232 11.911053
|
||||
8600 16738.487 -0.00084974054 0 5269.5227 11.911032
|
||||
8650 16738.486 0 0 5269.5233 11.911046
|
||||
8700 16738.486 0 0 5269.5234 11.91105
|
||||
8750 16738.486 0 0 5269.5235 11.911056
|
||||
8800 16738.486 0 0 5269.5235 11.911063
|
||||
8850 16738.487 -0.000227631 0 5269.5234 11.911065
|
||||
8900 16738.487 0 0 5269.5236 11.911068
|
||||
8950 16738.487 0 0 5269.5237 11.911058
|
||||
9000 16738.487 0 0 5269.5237 11.911045
|
||||
9050 16738.487 0 0 5269.5238 11.911036
|
||||
9100 16738.487 0 0 5269.5238 11.911034
|
||||
9150 16738.488 0 0 5269.5239 11.91104
|
||||
9200 16738.488 0 0 5269.5239 11.911052
|
||||
9250 16738.488 0 0 5269.524 11.911068
|
||||
9300 16738.488 0 0 5269.524 11.911079
|
||||
9350 16738.488 0 0 5269.5241 11.911078
|
||||
9400 16738.492 -0.0016306436 0 5269.5235 11.911038
|
||||
9450 16738.492 -0.0032567429 0 5269.522 11.911005
|
||||
9500 16738.495 -0.0036645351 0 5269.5224 11.910982
|
||||
9550 16738.49 -0.0010673912 0 5269.5237 11.911012
|
||||
9600 16738.489 0 0 5269.5244 11.911032
|
||||
9650 16738.489 0 0 5269.5244 11.911043
|
||||
9700 16738.49 0 0 5269.5245 11.911058
|
||||
9750 16738.49 0 0 5269.5245 11.911071
|
||||
9800 16738.49 0 0 5269.5246 11.911073
|
||||
9850 16738.49 0 0 5269.5246 11.911065
|
||||
9900 16738.49 0 0 5269.5247 11.911053
|
||||
9950 16738.491 -0.00058544643 0 5269.5243 11.911032
|
||||
10000 16738.493 -0.0015244931 0 5269.5242 11.911015
|
||||
Loop time of 2.30195 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 37533.440 tau/day, 4344.148 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0076839 | 0.0076839 | 0.0076839 | 0.0 | 0.33
|
||||
Neigh | 0.029562 | 0.029562 | 0.029562 | 0.0 | 1.28
|
||||
Comm | 0.0084877 | 0.0084877 | 0.0084877 | 0.0 | 0.37
|
||||
Output | 0.0037958 | 0.0037958 | 0.0037958 | 0.0 | 0.16
|
||||
Modify | 2.2446 | 2.2446 | 2.2446 | 0.0 | 97.51
|
||||
Other | | 0.00785 | | | 0.34
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 69 ave 69 max 69 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4 ave 4 max 4 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4
|
||||
Ave neighs/atom = 0.049382716
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:02
|
||||
329
examples/rigid/log.20Mar22.rigid.poems3.g++.4
Normal file
329
examples/rigid/log.20Mar22.rigid.poems3.g++.4
Normal file
@ -0,0 +1,329 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all poems file unconnected-bodies.dat
|
||||
WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035)
|
||||
9 clusters, 9 bodies, 0 joints, 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix poems command:
|
||||
|
||||
@Article{Mukherjee08,
|
||||
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
|
||||
title = {Substructured molecular dynamics using multibody dynamics algorithms},
|
||||
journal = {Intl.~J.~Non-linear Mechanics},
|
||||
year = 2008,
|
||||
volume = 43,
|
||||
pages = {1045--1055}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.686 571.71596 0 5265.8207 32.006226
|
||||
100 16298.5 136.65142 0 5267.6607 16.443791
|
||||
150 16682.639 17.488068 0 5269.43 14.900278
|
||||
200 16733.955 1.3724268 0 5269.4692 14.569123
|
||||
250 16738.877 -0.15250573 0 5269.4939 14.496287
|
||||
300 16738.611 -0.05516662 0 5269.5077 14.495909
|
||||
350 16738.515 -0.01744351 0 5269.5152 14.496329
|
||||
400 16738.488 -0.0060096677 0 5269.5178 14.496497
|
||||
450 16738.479 -0.0012712918 0 5269.5199 14.496575
|
||||
500 16738.479 -0.00081070354 0 5269.5203 14.49658
|
||||
550 16738.479 -0.00083205205 0 5269.5203 14.496577
|
||||
600 16738.479 -0.0005835658 0 5269.5206 14.49658
|
||||
650 16738.479 -0.00047227225 0 5269.5206 14.496583
|
||||
700 16738.479 0 0 5269.521 14.496593
|
||||
750 16738.479 0 0 5269.5211 14.496595
|
||||
800 16738.479 0 0 5269.5211 14.496596
|
||||
850 16738.479 0 0 5269.5211 14.496595
|
||||
900 16738.479 0 0 5269.5212 14.496593
|
||||
950 16738.485 -0.003532391 0 5269.5196 14.496546
|
||||
1000 16738.609 -0.051135033 0 5269.5109 14.496098
|
||||
1050 16737.381 0.32991002 0 5269.5055 14.525627
|
||||
1100 16737.915 0.16210932 0 5269.5058 14.531848
|
||||
1150 16738.726 -0.089235332 0 5269.5098 14.509768
|
||||
1200 16738.49 -0.0075446298 0 5269.5169 14.510489
|
||||
1250 16738.48 0 0 5269.5214 14.510585
|
||||
1300 16738.48 0 0 5269.5214 14.510587
|
||||
1350 16738.48 0 0 5269.5215 14.510588
|
||||
1400 16738.48 -0.00044742303 0 5269.5211 14.510581
|
||||
1450 16738.481 -0.0010975104 0 5269.5207 14.51057
|
||||
1500 16738.481 -0.00057925965 0 5269.5211 14.510575
|
||||
1550 16738.48 0 0 5269.5216 14.510582
|
||||
1600 16738.48 0 0 5269.5216 14.510581
|
||||
1650 16738.481 0 0 5269.5216 14.510581
|
||||
1700 16738.481 0 0 5269.5217 14.510582
|
||||
1750 16738.481 0 0 5269.5217 14.510583
|
||||
1800 16738.481 0 0 5269.5217 14.510585
|
||||
1850 16738.481 0 0 5269.5218 14.510585
|
||||
1900 16738.481 0 0 5269.5218 14.510585
|
||||
1950 16738.487 -0.0031700155 0 5269.5206 14.510534
|
||||
2000 16738.514 -0.013238802 0 5269.5188 14.510401
|
||||
2050 16738.578 -0.03654435 0 5269.5158 14.510155
|
||||
2100 16738.656 -0.063182323 0 5269.5137 14.510082
|
||||
2150 16738.63 -0.056004395 0 5269.5127 14.510096
|
||||
2200 16738.579 -0.038415873 0 5269.5143 14.510273
|
||||
2250 16738.538 -0.023709094 0 5269.516 14.510414
|
||||
2300 16738.512 -0.013252539 0 5269.5182 14.510501
|
||||
2350 16738.491 -0.0045593284 0 5269.5203 14.510598
|
||||
2400 16738.482 -0.00052242487 0 5269.5217 14.510655
|
||||
2450 16738.486 -0.0023245722 0 5269.5211 14.510627
|
||||
2500 16738.491 -0.005189304 0 5269.5197 14.510606
|
||||
2550 16738.604 -0.044988104 0 5269.5155 14.510185
|
||||
2600 16738.446 0.0009675401 0 5269.5117 14.510521
|
||||
2650 16732.887 1.753125 0 5269.5138 14.598792
|
||||
2700 16738.784 -0.10629556 0 5269.5107 14.499176
|
||||
2750 16734.136 1.359459 0 5269.5135 14.594678
|
||||
2800 16738.608 -0.047184149 0 5269.5147 14.510254
|
||||
2850 16738.509 -0.012527238 0 5269.5181 14.509344
|
||||
2900 16738.487 -0.0026065529 0 5269.521 14.509512
|
||||
2950 16738.498 -0.0082248532 0 5269.519 14.509457
|
||||
3000 16738.683 -0.071294028 0 5269.514 14.509005
|
||||
3050 16717.444 6.5874862 0 5269.4864 14.834144
|
||||
3100 16657.654 25.431253 0 5269.5074 14.467824
|
||||
3150 16739.322 -0.28964062 0 5269.497 13.658821
|
||||
3200 16733.615 1.4969789 0 5269.487 11.998304
|
||||
3250 16737.289 0.35071214 0 5269.4974 11.918931
|
||||
3300 16732.493 1.8663821 0 5269.503 12.109003
|
||||
3350 16738.717 -0.087719164 0 5269.5085 11.979747
|
||||
3400 16738.586 -0.045267897 0 5269.5095 11.97972
|
||||
3450 16738.662 -0.071274216 0 5269.5076 11.979564
|
||||
3500 16738.853 -0.13644992 0 5269.5026 11.979658
|
||||
3550 16729.612 2.7475277 0 5269.4774 12.195939
|
||||
3600 16728.659 3.059607 0 5269.4893 12.241248
|
||||
3650 16738.923 -0.15949792 0 5269.5014 11.991857
|
||||
3700 16738.76 -0.10695054 0 5269.5028 11.992932
|
||||
3750 16738.751 -0.10105954 0 5269.5057 11.993137
|
||||
3800 16738.597 -0.048627545 0 5269.5097 11.993456
|
||||
3850 16738.507 -0.016053927 0 5269.5138 11.992973
|
||||
3900 16738.485 -0.0060825487 0 5269.5169 11.993052
|
||||
3950 16738.475 -0.0014953722 0 5269.5183 11.993119
|
||||
4000 16738.472 -0.00054315391 0 5269.5184 11.99315
|
||||
4050 16738.472 -0.00023792126 0 5269.5187 11.993172
|
||||
4100 16738.472 0 0 5269.5189 11.993188
|
||||
4150 16738.472 0 0 5269.5189 11.993188
|
||||
4200 16738.472 0 0 5269.519 11.993178
|
||||
4250 16738.472 0 0 5269.519 11.993164
|
||||
4300 16738.472 0 0 5269.5191 11.993152
|
||||
4350 16738.473 0 0 5269.5191 11.993147
|
||||
4400 16738.473 0 0 5269.5192 11.993149
|
||||
4450 16738.473 0 0 5269.5192 11.993158
|
||||
4500 16738.473 0 0 5269.5193 11.99317
|
||||
4550 16738.473 0 0 5269.5193 11.993176
|
||||
4600 16738.473 0 0 5269.5194 11.993174
|
||||
4650 16738.473 0 0 5269.5194 11.993167
|
||||
4700 16738.474 0 0 5269.5195 11.993162
|
||||
4750 16738.474 0 0 5269.5195 11.99316
|
||||
4800 16738.474 0 0 5269.5196 11.99316
|
||||
4850 16738.474 0 0 5269.5196 11.993163
|
||||
4900 16738.474 0 0 5269.5197 11.99317
|
||||
4950 16738.474 0 0 5269.5197 11.993176
|
||||
5000 16738.475 0 0 5269.5198 11.993174
|
||||
5050 16738.475 0 0 5269.5198 11.993165
|
||||
5100 16738.475 0 0 5269.5199 11.993155
|
||||
5150 16738.475 0 0 5269.5199 11.99315
|
||||
5200 16738.475 0 0 5269.52 11.993153
|
||||
5250 16738.475 0 0 5269.52 11.993161
|
||||
5300 16738.476 0 0 5269.5201 11.993173
|
||||
5350 16738.476 0 0 5269.5201 11.993185
|
||||
5400 16738.476 0 0 5269.5202 11.993189
|
||||
5450 16738.476 0 0 5269.5202 11.993181
|
||||
5500 16738.476 0 0 5269.5203 11.993165
|
||||
5550 16738.483 -0.0030091905 0 5269.5195 11.993097
|
||||
5600 16738.534 -0.020777802 0 5269.5177 11.992799
|
||||
5650 16738.649 -0.059321662 0 5269.5153 11.993266
|
||||
5700 16409.08 103.75288 0 5269.5745 23.626238
|
||||
5750 16738.578 -0.036776519 0 5269.5155 11.910545
|
||||
5800 16738.484 -0.0047306177 0 5269.518 11.911008
|
||||
5850 16738.477 -0.00022082692 0 5269.5202 11.911078
|
||||
5900 16738.477 -0.00033136078 0 5269.5203 11.91107
|
||||
5950 16738.478 -0.00036902212 0 5269.5203 11.911052
|
||||
6000 16738.477 0 0 5269.5206 11.911044
|
||||
6050 16738.477 0 0 5269.5207 11.911034
|
||||
6100 16738.478 0 0 5269.5207 11.911032
|
||||
6150 16738.478 0 0 5269.5208 11.911037
|
||||
6200 16738.478 0 0 5269.5208 11.911049
|
||||
6250 16738.478 0 0 5269.5209 11.911062
|
||||
6300 16738.478 0 0 5269.5209 11.911068
|
||||
6350 16738.478 0 0 5269.521 11.911065
|
||||
6400 16738.478 0 0 5269.521 11.911058
|
||||
6450 16738.479 0 0 5269.5211 11.911052
|
||||
6500 16738.479 0 0 5269.5211 11.911047
|
||||
6550 16738.479 0 0 5269.5212 11.911046
|
||||
6600 16738.479 0 0 5269.5212 11.911049
|
||||
6650 16738.479 0 0 5269.5213 11.911056
|
||||
6700 16738.479 0 0 5269.5213 11.911062
|
||||
6750 16738.48 0 0 5269.5214 11.91106
|
||||
6800 16738.48 0 0 5269.5214 11.911051
|
||||
6850 16738.48 0 0 5269.5215 11.911044
|
||||
6900 16738.48 0 0 5269.5215 11.911041
|
||||
6950 16738.48 0 0 5269.5216 11.911045
|
||||
7000 16738.48 0 0 5269.5216 11.911053
|
||||
7050 16738.481 0 0 5269.5217 11.911063
|
||||
7100 16738.481 0 0 5269.5217 11.911071
|
||||
7150 16738.481 0 0 5269.5218 11.911072
|
||||
7200 16738.481 0 0 5269.5218 11.911063
|
||||
7250 16738.481 0 0 5269.5219 11.911048
|
||||
7300 16738.481 0 0 5269.5219 11.911036
|
||||
7350 16738.482 0 0 5269.522 11.911031
|
||||
7400 16738.482 0 0 5269.522 11.911035
|
||||
7450 16738.482 0 0 5269.5221 11.911046
|
||||
7500 16738.482 0 0 5269.5221 11.911062
|
||||
7550 16738.482 0 0 5269.5222 11.911077
|
||||
7600 16738.482 0 0 5269.5222 11.911081
|
||||
7650 16738.483 0 0 5269.5223 11.911071
|
||||
7700 16738.483 0 0 5269.5223 11.911054
|
||||
7750 16738.483 0 0 5269.5224 11.911039
|
||||
7800 16738.483 0 0 5269.5224 11.911031
|
||||
7850 16738.483 0 0 5269.5225 11.911031
|
||||
7900 16738.483 0 0 5269.5226 11.911039
|
||||
7950 16738.484 0 0 5269.5226 11.911052
|
||||
8000 16738.484 0 0 5269.5227 11.911065
|
||||
8050 16738.484 0 0 5269.5227 11.91107
|
||||
8100 16738.484 0 0 5269.5228 11.911065
|
||||
8150 16738.484 0 0 5269.5228 11.911056
|
||||
8200 16738.484 0 0 5269.5229 11.911047
|
||||
8250 16738.485 0 0 5269.5229 11.911042
|
||||
8300 16738.485 0 0 5269.523 11.911041
|
||||
8350 16738.485 0 0 5269.523 11.911046
|
||||
8400 16738.485 0 0 5269.5231 11.911055
|
||||
8450 16738.485 0 0 5269.5231 11.911062
|
||||
8500 16738.485 0 0 5269.5232 11.91106
|
||||
8550 16738.486 0 0 5269.5232 11.911053
|
||||
8600 16738.487 -0.00084974055 0 5269.5227 11.911032
|
||||
8650 16738.486 0 0 5269.5233 11.911046
|
||||
8700 16738.486 0 0 5269.5234 11.91105
|
||||
8750 16738.486 0 0 5269.5235 11.911056
|
||||
8800 16738.486 0 0 5269.5235 11.911063
|
||||
8850 16738.487 -0.000227631 0 5269.5234 11.911065
|
||||
8900 16738.487 0 0 5269.5236 11.911068
|
||||
8950 16738.487 0 0 5269.5237 11.911058
|
||||
9000 16738.487 0 0 5269.5237 11.911045
|
||||
9050 16738.487 0 0 5269.5238 11.911036
|
||||
9100 16738.487 0 0 5269.5238 11.911034
|
||||
9150 16738.488 0 0 5269.5239 11.91104
|
||||
9200 16738.488 0 0 5269.5239 11.911052
|
||||
9250 16738.488 0 0 5269.524 11.911068
|
||||
9300 16738.488 0 0 5269.524 11.911079
|
||||
9350 16738.488 0 0 5269.5241 11.911078
|
||||
9400 16738.492 -0.0016306433 0 5269.5235 11.911038
|
||||
9450 16738.492 -0.0032567425 0 5269.522 11.911005
|
||||
9500 16738.495 -0.0036645345 0 5269.5224 11.910982
|
||||
9550 16738.49 -0.001067391 0 5269.5237 11.911012
|
||||
9600 16738.489 0 0 5269.5244 11.911032
|
||||
9650 16738.489 0 0 5269.5244 11.911043
|
||||
9700 16738.49 0 0 5269.5245 11.911058
|
||||
9750 16738.49 0 0 5269.5245 11.911071
|
||||
9800 16738.49 0 0 5269.5246 11.911073
|
||||
9850 16738.49 0 0 5269.5246 11.911065
|
||||
9900 16738.49 0 0 5269.5247 11.911053
|
||||
9950 16738.491 -0.00058544648 0 5269.5243 11.911032
|
||||
10000 16738.493 -0.0015244933 0 5269.5242 11.911015
|
||||
Loop time of 2.36483 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 36535.358 tau/day, 4228.629 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0030635 | 0.0035263 | 0.0040903 | 0.7 | 0.15
|
||||
Neigh | 0.0093439 | 0.01002 | 0.010976 | 0.6 | 0.42
|
||||
Comm | 0.11912 | 0.12509 | 0.13346 | 1.5 | 5.29
|
||||
Output | 0.003411 | 0.0038449 | 0.0050123 | 1.1 | 0.16
|
||||
Modify | 2.1961 | 2.2052 | 2.2137 | 0.5 | 93.25
|
||||
Other | | 0.01717 | | | 0.73
|
||||
|
||||
Nlocal: 20.25 ave 27 max 9 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 31.5 ave 51 max 15 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 1 ave 4 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4
|
||||
Ave neighs/atom = 0.049382716
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
Total wall time: 0:00:02
|
||||
328
examples/rigid/log.20Mar22.rigid.poems4.g++.1
Normal file
328
examples/rigid/log.20Mar22.rigid.poems4.g++.1
Normal file
@ -0,0 +1,328 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems file connected-bodies.dat
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix poems command:
|
||||
|
||||
@Article{Mukherjee08,
|
||||
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
|
||||
title = {Substructured molecular dynamics using multibody dynamics algorithms},
|
||||
journal = {Intl.~J.~Non-linear Mechanics},
|
||||
year = 2008,
|
||||
volume = 43,
|
||||
pages = {1045--1055}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045742
|
||||
850 17821.483 711.53827 0 3681.7854 7.438428
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19374 0 3681.3037 11.787982
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184716
|
||||
1150 20849.582 206.01696 0 3680.9472 -0.86699118
|
||||
1200 21815.003 45.317409 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064083
|
||||
1300 20780.781 217.36511 0 3680.8286 6.0538604
|
||||
1350 20558.971 254.36489 0 3680.8601 -3.6773868
|
||||
1400 21485.029 99.812844 0 3680.6511 -16.185479
|
||||
1450 21771.107 52.159653 0 3680.6775 -2.4756655
|
||||
1500 21520.949 93.503876 0 3680.3286 2.1023573
|
||||
1550 21351.419 121.6813 0 3680.2511 5.5159876
|
||||
1600 20778.804 216.92191 0 3680.0559 15.089203
|
||||
1650 21477.636 100.21873 0 3679.8247 -1.1045277
|
||||
1700 18501.33 596.4807 0 3680.0357 -15.6798
|
||||
1750 18563.64 587.34824 0 3681.2882 33.532308
|
||||
1800 19110.175 494.82517 0 3679.8543 18.024074
|
||||
1850 21364.178 119.23765 0 3679.9339 2.5290144
|
||||
1900 20146.588 322.15509 0 3679.9197 5.7317299
|
||||
1950 20692.676 231.25264 0 3680.0319 4.297803
|
||||
2000 20943.902 189.11251 0 3679.7629 -22.643824
|
||||
2050 19667.823 401.86882 0 3679.8394 3.6241915
|
||||
2100 20280.125 299.81485 0 3679.8357 7.4804047
|
||||
2150 19181.201 483.6306 0 3680.4975 22.63342
|
||||
2200 21301.144 130.54014 0 3680.7308 4.7074288
|
||||
2250 20484.876 266.98315 0 3681.1291 -8.6578278
|
||||
2300 18648.161 573.07329 0 3681.1001 -5.2550954
|
||||
2350 21515.748 95.243054 0 3681.201 -9.386512
|
||||
2400 21462.551 104.18267 0 3681.2745 -29.46442
|
||||
2450 20107.732 330.99437 0 3682.2831 35.38497
|
||||
2500 20771.509 220.47713 0 3682.3953 -12.324858
|
||||
2550 20499.887 265.58494 0 3682.2327 -22.713874
|
||||
2600 21462.182 105.24427 0 3682.2747 -10.175788
|
||||
2650 21004.949 181.51383 0 3682.3387 4.949195
|
||||
2700 18673.552 570.45017 0 3682.7089 21.201437
|
||||
2750 21257.562 139.198 0 3682.1249 -7.5793039
|
||||
2800 21559.645 88.844759 0 3682.119 -6.2360467
|
||||
2850 20865.227 204.46262 0 3682.0004 0.39575069
|
||||
2900 19428.614 443.93293 0 3682.0352 12.796676
|
||||
2950 19630.1 410.18487 0 3681.8681 -0.50572623
|
||||
3000 19663.218 404.06316 0 3681.2661 6.0827093
|
||||
3050 19087.572 500.8452 0 3682.1073 -6.3526476
|
||||
3100 18229.94 643.77681 0 3682.1001 11.453637
|
||||
3150 18927.492 527.51919 0 3682.1011 -1.662863
|
||||
3200 18320.514 628.55895 0 3681.978 21.176126
|
||||
3250 18204.677 647.96462 0 3682.0775 11.331521
|
||||
3300 19231.978 477.02117 0 3682.3509 3.8381593
|
||||
3350 18153.44 656.70376 0 3682.2772 15.135615
|
||||
3400 17476.768 770.0598 0 3682.8545 -3.394312
|
||||
3450 21097.531 166.17241 0 3682.4276 3.74301
|
||||
3500 17605.784 747.54808 0 3681.8454 3.3420627
|
||||
3550 19238.34 476.00608 0 3682.3961 1.1413836
|
||||
3600 18155.288 656.57434 0 3682.4557 3.4360446
|
||||
3650 18735.622 559.2377 0 3681.8413 28.760363
|
||||
3700 15310.261 1134.4215 0 3686.1317 44.207018
|
||||
3750 15377.116 1123.4786 0 3686.3313 7.6773215
|
||||
3800 18798.895 549.05928 0 3682.2084 -12.905825
|
||||
3850 18322.563 628.87744 0 3682.6379 -16.067793
|
||||
3900 19963.049 355.65441 0 3682.8292 3.4694064
|
||||
3950 19925.48 361.2507 0 3682.1641 5.0058567
|
||||
4000 19141.423 492.41081 0 3682.648 -12.782769
|
||||
4050 20022.241 345.61655 0 3682.6568 -3.0149905
|
||||
4100 21348.635 124.95646 0 3683.0624 -4.85779
|
||||
4150 21011.812 181.1132 0 3683.0819 -3.9526196
|
||||
4200 20222.276 312.63945 0 3683.0187 -23.63437
|
||||
4250 20957.757 189.77152 0 3682.731 -1.3712469
|
||||
4300 20070.215 337.5751 0 3682.611 -6.8816517
|
||||
4350 21322.437 129.09228 0 3682.8318 -6.9442178
|
||||
4400 19440.445 442.77531 0 3682.8495 -0.11606236
|
||||
4450 20964.516 188.67174 0 3682.7577 4.8533525
|
||||
4500 13530.08 1428.5497 0 3683.563 12.333187
|
||||
4550 20461.637 272.58882 0 3682.8616 4.5111943
|
||||
4600 17072.994 836.58228 0 3682.0812 5.7611617
|
||||
4650 18860.748 539.82027 0 3683.2782 -2.5558958
|
||||
4700 18373.927 621.04093 0 3683.3621 5.4020702
|
||||
4750 20321.437 296.63662 0 3683.5428 8.9571617
|
||||
4800 21083.122 169.84086 0 3683.6946 10.566368
|
||||
4850 20499.669 267.7012 0 3684.3128 4.2924237
|
||||
4900 20308.781 300.38168 0 3685.1785 -12.396923
|
||||
4950 21043.303 178.56295 0 3685.7801 3.8923762
|
||||
5000 20718.383 232.52208 0 3685.5859 -12.43234
|
||||
5050 21005.749 184.4363 0 3685.3945 -7.6463487
|
||||
5100 20714.133 233.27745 0 3685.6329 -1.6944135
|
||||
5150 19577.452 422.73035 0 3685.639 -21.831219
|
||||
5200 14044.647 1343.9545 0 3684.729 -6.8407194
|
||||
5250 19089.805 504.0893 0 3685.7235 4.05641
|
||||
5300 21094.745 169.94699 0 3685.7378 -0.66593212
|
||||
5350 19907.559 366.77598 0 3684.7024 1.5248525
|
||||
5400 20382.81 289.13263 0 3686.2676 -11.919321
|
||||
5450 19593.693 420.70548 0 3686.3209 -1.1568628
|
||||
5500 20906.08 202.09801 0 3686.4447 -2.4284971
|
||||
5550 16315.465 965.56973 0 3684.8138 -33.178221
|
||||
5600 19714.57 400.39687 0 3686.1586 19.950231
|
||||
5650 20561.724 259.54797 0 3686.502 8.2074524
|
||||
5700 19349.502 460.7789 0 3685.6959 16.252649
|
||||
5750 21006.818 185.56805 0 3686.7044 -11.96089
|
||||
5800 20268.2 307.97547 0 3686.0089 17.322311
|
||||
5850 21018.322 184.16179 0 3687.2154 -14.379909
|
||||
5900 19695.647 404.57094 0 3687.1787 -20.718904
|
||||
5950 21021.687 183.66311 0 3687.2776 -15.206081
|
||||
6000 18947.535 529.30554 0 3687.2281 17.863927
|
||||
6050 15272.373 1141.012 0 3686.4075 -0.43375666
|
||||
6100 17766.197 721.75792 0 3682.7908 11.378913
|
||||
6150 18612.573 584.06688 0 3686.1623 17.543241
|
||||
6200 19005.155 518.97146 0 3686.4973 -16.223107
|
||||
6250 20997.507 187.55499 0 3687.1394 -11.613546
|
||||
6300 19639.901 413.58048 0 3686.8974 14.407136
|
||||
6350 19580.399 423.02818 0 3686.428 -5.5801796
|
||||
6400 14134.119 1332.0662 0 3687.7527 84.864425
|
||||
6450 21598.824 87.419966 0 3687.224 -5.8358352
|
||||
6500 18208.216 649.29108 0 3683.9938 -8.1510884
|
||||
6550 19364.586 459.59813 0 3687.0291 -12.053563
|
||||
6600 20710.927 235.11914 0 3686.9403 -1.0470193
|
||||
6650 21132.334 165.08091 0 3687.1366 1.0785471
|
||||
6700 20217.285 317.589 0 3687.1365 0.055447462
|
||||
6750 21232.279 148.57412 0 3687.2873 -2.4551657
|
||||
6800 20292.683 304.76539 0 3686.8793 -0.42311295
|
||||
6850 19056.291 510.49927 0 3686.5478 6.9533826
|
||||
6900 20429.82 282.23764 0 3687.2076 -4.2360112
|
||||
6950 21281.278 140.27361 0 3687.1533 -0.07475261
|
||||
7000 17173.388 824.54446 0 3686.7758 10.753828
|
||||
7050 18079.7 674.56274 0 3687.846 12.975804
|
||||
7100 16433.233 950.73904 0 3689.6112 -10.5102
|
||||
7150 19033.335 515.59672 0 3687.8193 0.29109447
|
||||
7200 17286.428 809.02352 0 3690.0948 2.3015698
|
||||
7250 16811.962 886.6645 0 3688.6582 -7.4787512
|
||||
7300 15992.461 1023.4849 0 3688.895 -5.2354222
|
||||
7350 19211.451 487.63129 0 3689.5398 8.4351737
|
||||
7400 19065.682 511.95629 0 3689.57 -12.47448
|
||||
7450 21369.265 128.10098 0 3689.6451 2.2930546
|
||||
7500 16807.109 888.64602 0 3689.8308 14.761969
|
||||
7550 18063.046 679.21873 0 3689.7264 3.8950434
|
||||
7600 17794.987 724.55404 0 3690.3851 14.379016
|
||||
7650 17904.751 706.14354 0 3690.2688 23.813776
|
||||
7700 19670.09 411.3021 0 3689.6504 14.099245
|
||||
7750 18082.562 675.23975 0 3689.0001 15.788521
|
||||
7800 17776.135 726.91445 0 3689.6037 6.9780735
|
||||
7850 17062.575 846.33412 0 3690.0966 -8.9289256
|
||||
7900 19059.2 513.07737 0 3689.6107 16.992843
|
||||
7950 16269.685 978.48914 0 3690.1033 11.180179
|
||||
8000 20115.278 336.91405 0 3689.4604 -6.4882518
|
||||
8050 21173.72 161.15229 0 3690.1056 -2.2164491
|
||||
8100 19238.235 484.42784 0 3690.8004 23.412709
|
||||
8150 18438.4 617.58743 0 3690.6542 0.89156316
|
||||
8200 21438.764 117.12721 0 3690.2546 -1.7193227
|
||||
8250 21195.806 157.66607 0 3690.3003 3.820447
|
||||
8300 21177.549 161.13702 0 3690.7286 0.94938203
|
||||
8350 21060.267 181.06887 0 3691.1135 2.8179025
|
||||
8400 20087.113 343.46206 0 3691.3142 8.1484473
|
||||
8450 19298.478 474.87133 0 3691.2843 -16.239664
|
||||
8500 21654.353 82.083485 0 3691.1423 -8.1464138
|
||||
8550 19920.544 371.34795 0 3691.4386 20.765144
|
||||
8600 21692.293 75.655154 0 3691.0373 -13.316763
|
||||
8650 21231.322 151.8989 0 3690.4526 -11.388238
|
||||
8700 19530.647 434.89585 0 3690.0037 2.7433786
|
||||
8750 19720.63 403.07773 0 3689.8493 -6.416414
|
||||
8800 21321.378 136.04091 0 3689.604 1.3661635
|
||||
8850 19811.906 387.80489 0 3689.7893 3.704143
|
||||
8900 19734.167 400.92444 0 3689.9523 2.5685155
|
||||
8950 21076.459 177.18119 0 3689.9244 -11.939513
|
||||
9000 20967.246 195.42966 0 3689.9707 2.0092705
|
||||
9050 21122.023 169.62103 0 3689.9582 2.3791301
|
||||
9100 20169.346 328.27229 0 3689.8299 -3.5017988
|
||||
9150 21418.641 119.84513 0 3689.6187 2.486073
|
||||
9200 20876.042 210.26452 0 3689.6048 -5.3839897
|
||||
9250 21572.38 93.74407 0 3689.1407 -8.3676952
|
||||
9300 20944.78 197.98577 0 3688.7824 1.3278314
|
||||
9350 20706.52 237.48767 0 3688.5744 4.6944204
|
||||
9400 16412.314 953.47251 0 3688.8581 26.134976
|
||||
9450 20461.68 277.76243 0 3688.0424 17.647445
|
||||
9500 20893.994 205.64261 0 3687.9749 -10.642418
|
||||
9550 20503.447 270.63504 0 3687.8761 -17.769897
|
||||
9600 19677.799 408.05887 0 3687.692 -2.7938604
|
||||
9650 17480.971 774.1855 0 3687.6806 0.59827043
|
||||
9700 17799.126 721.50817 0 3688.0292 44.387928
|
||||
9750 20443.384 280.16837 0 3687.399 3.0619324
|
||||
9800 20545.255 263.40108 0 3687.6102 3.6229381
|
||||
9850 20722.819 233.57142 0 3687.3745 0.86462694
|
||||
9900 21128.462 165.09767 0 3686.508 -6.9636843
|
||||
9950 21343.307 130.46714 0 3687.685 -9.7382705
|
||||
10000 20623.887 250.37866 0 3687.6932 2.7529835
|
||||
Loop time of 2.28812 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 37760.318 tau/day, 4370.407 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.094122 | 0.094122 | 0.094122 | 0.0 | 4.11
|
||||
Neigh | 0.076427 | 0.076427 | 0.076427 | 0.0 | 3.34
|
||||
Comm | 0.0066867 | 0.0066867 | 0.0066867 | 0.0 | 0.29
|
||||
Output | 0.003606 | 0.003606 | 0.003606 | 0.0 | 0.16
|
||||
Modify | 2.0986 | 2.0986 | 2.0986 | 0.0 | 91.72
|
||||
Other | | 0.008698 | | | 0.38
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 62 ave 62 max 62 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 905 ave 905 max 905 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 905
|
||||
Ave neighs/atom = 11.17284
|
||||
Neighbor list builds = 991
|
||||
Dangerous builds = 927
|
||||
Total wall time: 0:00:02
|
||||
328
examples/rigid/log.20Mar22.rigid.poems4.g++.4
Normal file
328
examples/rigid/log.20Mar22.rigid.poems4.g++.4
Normal file
@ -0,0 +1,328 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems file connected-bodies.dat
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix poems command:
|
||||
|
||||
@Article{Mukherjee08,
|
||||
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
|
||||
title = {Substructured molecular dynamics using multibody dynamics algorithms},
|
||||
journal = {Intl.~J.~Non-linear Mechanics},
|
||||
year = 2008,
|
||||
volume = 43,
|
||||
pages = {1045--1055}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045742
|
||||
850 17821.483 711.53827 0 3681.7854 7.4384281
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19374 0 3681.3037 11.787982
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184716
|
||||
1150 20849.582 206.01696 0 3680.9472 -0.86699115
|
||||
1200 21815.003 45.317409 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064083
|
||||
1300 20780.781 217.36511 0 3680.8286 6.0538606
|
||||
1350 20558.971 254.36489 0 3680.8601 -3.6773868
|
||||
1400 21485.03 99.812843 0 3680.6511 -16.185479
|
||||
1450 21771.107 52.159652 0 3680.6775 -2.4756656
|
||||
1500 21520.949 93.503872 0 3680.3286 2.1023574
|
||||
1550 21351.419 121.68131 0 3680.2511 5.5159875
|
||||
1600 20778.804 216.92191 0 3680.0559 15.089203
|
||||
1650 21477.636 100.21877 0 3679.8247 -1.104524
|
||||
1700 18501.329 596.48084 0 3680.0357 -15.679806
|
||||
1750 18563.639 587.34841 0 3681.2882 33.532316
|
||||
1800 19110.174 494.82524 0 3679.8543 18.024079
|
||||
1850 21364.178 119.23767 0 3679.9339 2.5290075
|
||||
1900 20146.588 322.15506 0 3679.9197 5.7317368
|
||||
1950 20692.674 231.25288 0 3680.0319 4.2977982
|
||||
2000 20943.904 189.11229 0 3679.7629 -22.643749
|
||||
2050 19667.815 401.87016 0 3679.8394 3.6240972
|
||||
2100 20280.109 299.81759 0 3679.8357 7.4803647
|
||||
2150 19181.146 483.63975 0 3680.4974 22.634167
|
||||
2200 21301.194 130.53171 0 3680.7308 4.7072523
|
||||
2250 20484.79 266.99736 0 3681.1291 -8.6583002
|
||||
2300 18648.002 573.09962 0 3681.1 -5.2548835
|
||||
2350 21515.851 95.225745 0 3681.2009 -9.3875216
|
||||
2400 21462.37 104.21272 0 3681.2744 -29.459857
|
||||
2450 20108.034 330.94394 0 3682.2829 35.37058
|
||||
2500 20771.818 220.42545 0 3682.3951 -12.318936
|
||||
2550 20502.815 265.09577 0 3682.2316 -22.726822
|
||||
2600 21462.006 105.2733 0 3682.2744 -10.180394
|
||||
2650 21009.656 180.72738 0 3682.3367 4.9580828
|
||||
2700 18680.012 569.37179 0 3682.7071 21.114114
|
||||
2750 21256.19 139.42201 0 3682.1203 -7.4744399
|
||||
2800 21552.267 90.071446 0 3682.1159 -6.2906304
|
||||
2850 20879.958 202.00905 0 3682.0021 0.57990903
|
||||
2900 19018.645 512.35214 0 3682.1262 13.883084
|
||||
2950 19819.365 378.55747 0 3681.785 -0.7348943
|
||||
3000 20269.229 303.35149 0 3681.5563 6.3088075
|
||||
3050 19236.727 475.99457 0 3682.1158 -10.703575
|
||||
3100 18391.55 616.96976 0 3682.2281 9.850079
|
||||
3150 20258.563 305.82076 0 3682.248 7.1951283
|
||||
3200 20716.384 229.15502 0 3681.8856 2.9042294
|
||||
3250 18662.237 572.0784 0 3682.4512 9.2108597
|
||||
3300 19162.278 488.60646 0 3682.3195 3.3306562
|
||||
3350 21235.679 142.98279 0 3682.2626 0.29397483
|
||||
3400 17677.053 736.09247 0 3682.2679 32.75269
|
||||
3450 20852.392 206.65618 0 3682.0548 -4.8319056
|
||||
3500 21182.918 151.46754 0 3681.9539 -5.6330382
|
||||
3550 20589.85 250.40724 0 3682.049 12.582133
|
||||
3600 20973.659 186.28043 0 3681.8903 10.935266
|
||||
3650 17838.632 707.92145 0 3681.0268 -17.200926
|
||||
3700 21538.002 92.744409 0 3682.4114 -0.72124229
|
||||
3750 21390.294 117.90865 0 3682.9576 -7.8431786
|
||||
3800 17921.046 696.50311 0 3683.344 -9.4641531
|
||||
3850 20356.471 290.22624 0 3682.9715 2.4593463
|
||||
3900 20374.077 287.10249 0 3682.782 -1.9519082
|
||||
3950 20563.915 255.29993 0 3682.619 -6.124649
|
||||
4000 20991.467 184.76183 0 3683.3397 1.8954961
|
||||
4050 17805.623 716.24698 0 3683.8509 -20.454944
|
||||
4100 19916.389 363.86301 0 3683.2611 -0.27912557
|
||||
4150 19221.623 480.01232 0 3683.6161 -11.562492
|
||||
4200 20526.82 261.78571 0 3682.9224 -3.9522917
|
||||
4250 20922.813 196.1799 0 3683.3154 0.11947446
|
||||
4300 19956.66 357.78133 0 3683.8914 19.156093
|
||||
4350 19735.73 394.45981 0 3683.7482 14.865775
|
||||
4400 21702.656 67.099805 0 3684.2092 -13.502538
|
||||
4450 18163.055 656.97231 0 3684.1482 -0.6243111
|
||||
4500 17477.718 771.25976 0 3684.2127 -0.4664004
|
||||
4550 20676.507 238.19814 0 3684.2827 -19.444969
|
||||
4600 17322.922 796.77058 0 3683.9242 27.003966
|
||||
4650 11905.158 1704.9151 0 3689.1082 15.574169
|
||||
4700 18689.079 569.80982 0 3684.6563 -14.67311
|
||||
4750 19821.745 381.01914 0 3684.6433 5.0436795
|
||||
4800 20621.335 247.96269 0 3684.8518 -16.407263
|
||||
4850 21923.814 30.965964 0 3684.935 -13.418244
|
||||
4900 18840.555 544.41538 0 3684.5079 11.005357
|
||||
4950 15366.601 1124.2481 0 3685.3482 17.412375
|
||||
5000 18274.314 639.01311 0 3684.732 5.3261109
|
||||
5050 21173.687 155.83673 0 3684.7845 5.4056809
|
||||
5100 21738.219 61.75201 0 3684.7885 -2.631945
|
||||
5150 16597.949 918.84841 0 3685.1732 -10.124101
|
||||
5200 20752.758 225.95919 0 3684.7522 -5.2441372
|
||||
5250 17652.088 741.2645 0 3683.2793 2.0080739
|
||||
5300 19907.523 366.53115 0 3684.4516 8.4266792
|
||||
5350 20104.189 334.14522 0 3684.8433 17.21925
|
||||
5400 21499.848 101.71631 0 3685.0243 -6.1103541
|
||||
5450 21203.533 151.14574 0 3685.068 -5.9468503
|
||||
5500 21076.513 172.45652 0 3685.2088 5.1418181
|
||||
5550 20158.398 325.56609 0 3685.2992 -1.6486034
|
||||
5600 20787.836 221.19563 0 3685.835 -10.66805
|
||||
5650 19687.154 404.77204 0 3685.9644 -23.49128
|
||||
5700 20419.311 282.58328 0 3685.8017 -0.52808211
|
||||
5750 19738.522 395.95893 0 3685.7126 1.3889817
|
||||
5800 18300.025 635.66905 0 3685.6732 23.490447
|
||||
5850 20585.004 255.02032 0 3685.8543 -0.20699939
|
||||
5900 20373.839 290.15881 0 3685.7987 -7.9712187
|
||||
5950 18163.832 659.91192 0 3687.2173 5.4494586
|
||||
6000 21049.247 177.43029 0 3685.6382 2.9138342
|
||||
6050 21239.803 145.77613 0 3685.7433 -1.4927769
|
||||
6100 20686.361 237.86454 0 3685.5913 -0.95516297
|
||||
6150 20461.754 275.31546 0 3685.6079 -3.4166412
|
||||
6200 19264.208 474.73017 0 3685.4316 11.750757
|
||||
6250 21180.813 155.31746 0 3685.4529 2.8188219
|
||||
6300 21047.543 177.4394 0 3685.3632 1.8641486
|
||||
6350 20232.576 313.17716 0 3685.2731 2.8150209
|
||||
6400 20185.616 321.33454 0 3685.6038 -3.8697311
|
||||
6450 18969.632 523.95865 0 3685.5639 0.6725512
|
||||
6500 17592.574 753.49959 0 3685.5952 -1.2557393
|
||||
6550 21279.049 138.42524 0 3684.9335 -1.208945
|
||||
6600 21408.457 116.4143 0 3684.4904 -1.5332953
|
||||
6650 19758.218 391.17316 0 3684.2096 1.8511312
|
||||
6700 20766.943 223.44631 0 3684.6036 -2.3672623
|
||||
6750 20399.631 284.09914 0 3684.0377 -5.4089876
|
||||
6800 21296.628 135.14662 0 3684.5847 -3.8442549
|
||||
6850 20641.481 244.4451 0 3684.692 1.4020639
|
||||
6900 20852.81 209.23009 0 3684.6984 1.8512104
|
||||
6950 20940.555 194.66882 0 3684.7614 -6.554676
|
||||
7000 19496.988 435.28199 0 3684.78 -15.120269
|
||||
7050 19796.829 385.04227 0 3684.5138 -4.1068804
|
||||
7100 19945.264 360.42431 0 3684.635 -4.0629042
|
||||
7150 19431.123 446.12911 0 3684.6497 -6.8321751
|
||||
7200 16864.851 873.80043 0 3684.6089 14.309069
|
||||
7250 20438.75 277.85982 0 3684.3181 -11.41223
|
||||
7300 17688.684 734.01576 0 3682.1298 35.938373
|
||||
7350 21573.419 88.63421 0 3684.204 -3.9032749
|
||||
7400 21198.486 150.72249 0 3683.8034 -7.1477117
|
||||
7450 20586.708 252.93928 0 3684.0572 -7.6634645
|
||||
7500 21815.377 48.180377 0 3684.0765 0.97457507
|
||||
7550 17791.352 718.87564 0 3684.101 28.248235
|
||||
7600 21828.874 45.928597 0 3684.0742 -0.25814944
|
||||
7650 20827.961 212.35674 0 3683.6835 -3.4083384
|
||||
7700 21319.176 130.43547 0 3683.6315 -12.434856
|
||||
7750 20127.904 328.69643 0 3683.3471 -16.975711
|
||||
7800 21741.772 59.679206 0 3683.3078 3.6261863
|
||||
7850 19612.334 414.37418 0 3683.0964 1.3763274
|
||||
7900 20071.318 337.74624 0 3682.9658 -0.40982763
|
||||
7950 17925.664 695.29582 0 3682.9065 17.104439
|
||||
8000 19125.978 492.76383 0 3680.4268 10.807662
|
||||
8050 20233.848 310.42681 0 3682.7347 13.386237
|
||||
8100 20551.619 257.86699 0 3683.1368 -13.97515
|
||||
8150 21578.323 86.88362 0 3683.2708 -9.6811587
|
||||
8200 21154.833 157.72897 0 3683.5344 0.62312375
|
||||
8250 21321.143 129.83967 0 3683.3636 1.9536438
|
||||
8300 21041.696 176.04177 0 3682.9911 4.7475567
|
||||
8350 19883.39 369.32649 0 3683.2247 -7.0959328
|
||||
8400 21626.067 79.062992 0 3683.4075 -14.919059
|
||||
8450 21375.201 120.86836 0 3683.4019 -5.3461514
|
||||
8500 20281.059 303.10304 0 3683.2796 3.7975093
|
||||
8550 21170.533 154.48432 0 3682.9065 -1.1568561
|
||||
8600 17754.931 724.00158 0 3683.1568 14.15254
|
||||
8650 20685.478 235.65879 0 3683.2385 -5.2694179
|
||||
8700 21489.165 101.90509 0 3683.4326 -4.2510612
|
||||
8750 21106.682 165.41638 0 3683.1968 -3.9186708
|
||||
8800 19149.516 491.5843 0 3683.1702 -11.419849
|
||||
8850 21451.865 108.1814 0 3683.4923 -7.8256219
|
||||
8900 19567.4 421.81206 0 3683.0454 -0.71997056
|
||||
8950 20934.097 194.48033 0 3683.4965 -7.0106879
|
||||
9000 18531.559 595.25957 0 3683.8528 3.7449399
|
||||
9050 18868.821 537.22549 0 3682.029 9.9926092
|
||||
9100 19972.527 354.73119 0 3683.4858 -0.30871263
|
||||
9150 19641.651 409.18618 0 3682.7947 -1.3036238
|
||||
9200 20019.08 346.19657 0 3682.7099 6.7425386
|
||||
9250 19259.286 473.04973 0 3682.9308 -24.120659
|
||||
9300 21597.757 82.971857 0 3682.598 -13.748483
|
||||
9350 19348.379 457.23576 0 3681.9656 3.1571402
|
||||
9400 19129.588 493.35235 0 3681.617 8.6293783
|
||||
9450 20337.025 291.20959 0 3680.7138 6.8590795
|
||||
9500 20581.788 249.65891 0 3679.9569 -18.892836
|
||||
9550 19482.069 433.0077 0 3680.0192 23.029778
|
||||
9600 19182.794 482.96871 0 3680.101 -11.081731
|
||||
9650 20086.771 332.5311 0 3680.3263 -18.939681
|
||||
9700 20274.046 300.98818 0 3679.9959 6.7538762
|
||||
9750 18743.595 555.08045 0 3679.0129 8.2757138
|
||||
9800 19464.311 435.66288 0 3679.7148 7.0528759
|
||||
9850 21249.848 138.27382 0 3679.9152 -10.847402
|
||||
9900 21156.214 153.84621 0 3679.8819 -7.8359674
|
||||
9950 21643.134 72.547515 0 3679.7365 -10.507744
|
||||
10000 19587.948 414.64942 0 3679.3075 6.1173553
|
||||
Loop time of 2.35562 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 36678.236 tau/day, 4245.166 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0055581 | 0.024882 | 0.055326 | 12.0 | 1.06
|
||||
Neigh | 0.0073809 | 0.022107 | 0.043683 | 9.2 | 0.94
|
||||
Comm | 0.12484 | 0.14528 | 0.1833 | 6.2 | 6.17
|
||||
Output | 0.0035526 | 0.0041048 | 0.0055462 | 1.3 | 0.17
|
||||
Modify | 2.1078 | 2.1414 | 2.162 | 1.5 | 90.91
|
||||
Other | | 0.0178 | | | 0.76
|
||||
|
||||
Nlocal: 20.25 ave 81 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 41 ave 78 max 11 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 193.5 ave 774 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 774
|
||||
Ave neighs/atom = 9.5555556
|
||||
Neighbor list builds = 989
|
||||
Dangerous builds = 915
|
||||
Total wall time: 0:00:02
|
||||
329
examples/rigid/log.20Mar22.rigid.poems5.g++.1
Normal file
329
examples/rigid/log.20Mar22.rigid.poems5.g++.1
Normal file
@ -0,0 +1,329 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems file connected-bodies2.dat
|
||||
2 clusters, 9 bodies, 7 joints, 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix poems command:
|
||||
|
||||
@Article{Mukherjee08,
|
||||
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
|
||||
title = {Substructured molecular dynamics using multibody dynamics algorithms},
|
||||
journal = {Intl.~J.~Non-linear Mechanics},
|
||||
year = 2008,
|
||||
volume = 43,
|
||||
pages = {1045--1055}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -2.7403788
|
||||
50 12774.759 1538.7382 0 3904.4344 18.086359
|
||||
100 19803.641 237.21132 0 3904.5523 -3.1528278
|
||||
150 20259.6 152.62072 0 3904.3985 -4.6173524
|
||||
200 20705.978 69.977442 0 3904.4178 9.0928158
|
||||
250 19552.211 283.50525 0 3904.285 15.670465
|
||||
300 19266.324 333.5792 0 3901.4169 7.2119197
|
||||
350 20738.325 63.738945 0 3904.1694 -23.03999
|
||||
400 20616.682 86.082444 0 3903.9864 -13.783584
|
||||
450 19831.326 230.13858 0 3902.6063 0.42074361
|
||||
500 20365.825 131.47231 0 3902.9213 0.6921524
|
||||
550 20794.102 52.163238 0 3902.9229 4.5895354
|
||||
600 20853.873 40.899172 0 3902.7275 2.3593042
|
||||
650 19255.802 336.29509 0 3902.1844 10.341742
|
||||
700 18526.969 471.02462 0 3901.9448 -0.61898691
|
||||
750 18960.662 391.26068 0 3902.4944 12.04731
|
||||
800 20142.432 172.05177 0 3902.1317 4.6838621
|
||||
850 19932.48 210.71175 0 3901.9118 3.4716043
|
||||
900 20243.528 153.13972 0 3901.9411 3.6490762
|
||||
950 20388.132 126.88722 0 3902.4671 -4.4518463
|
||||
1000 20076.333 184.61915 0 3902.4586 -2.272315
|
||||
1050 20859.506 39.696993 0 3902.5684 6.45166
|
||||
1100 15284.661 1072.1908 0 3902.6836 21.194042
|
||||
1150 19658.317 261.99809 0 3902.4272 -2.874422
|
||||
1200 20767.681 56.717094 0 3902.5839 -34.817444
|
||||
1250 20625.583 82.586399 0 3902.1388 11.697329
|
||||
1300 20690.013 71.006478 0 3902.4903 -29.292777
|
||||
1350 20936.019 26.022786 0 3903.0634 1.0316025
|
||||
1400 19753.559 244.81785 0 3902.8844 6.7138514
|
||||
1450 15690.149 998.342 0 3903.9252 48.124557
|
||||
1500 20234.455 155.92516 0 3903.0465 13.17221
|
||||
1550 20779.631 55.063009 0 3903.1428 -2.639045
|
||||
1600 20642.753 80.233905 0 3902.9659 -2.4688467
|
||||
1650 18785.696 423.90402 0 3902.7365 -5.6466663
|
||||
1700 20965.076 20.760444 0 3903.182 -0.45364296
|
||||
1750 18935.406 396.96067 0 3903.5173 25.913302
|
||||
1800 20581.559 91.756972 0 3903.1567 3.8217234
|
||||
1850 20616.946 85.184849 0 3903.1378 4.1907972
|
||||
1900 16602.053 828.40949 0 3902.8637 -0.49505122
|
||||
1950 20175.526 166.53362 0 3902.7421 5.603825
|
||||
2000 20261.924 150.39322 0 3902.6014 -1.196958
|
||||
2050 20170.339 167.40504 0 3902.6531 -0.80849882
|
||||
2100 19820.132 231.26755 0 3901.6624 3.1476607
|
||||
2150 20666.19 75.838461 0 3902.9106 0.53899287
|
||||
2200 19873.51 222.53286 0 3902.8124 7.9310276
|
||||
2250 18548.063 467.69698 0 3902.5235 16.905356
|
||||
2300 20616.61 84.762399 0 3902.6531 -6.7872951
|
||||
2350 18167.738 538.13635 0 3902.5322 -11.458285
|
||||
2400 20120.227 177.01954 0 3902.9875 -1.2593018
|
||||
2450 20436.599 118.32469 0 3902.8801 -6.5989174
|
||||
2500 18919.923 400.26361 0 3903.9531 32.37476
|
||||
2550 19675.809 259.77151 0 3903.4398 19.437327
|
||||
2600 19739.842 247.86388 0 3903.3901 -7.519784
|
||||
2650 20557.026 96.530313 0 3903.387 0.60211646
|
||||
2700 20666.602 76.099892 0 3903.2484 0.16825503
|
||||
2750 20924.585 28.453883 0 3903.3771 2.4227171
|
||||
2800 20360.659 132.8596 0 3903.352 4.1440877
|
||||
2850 20783.475 54.518625 0 3903.3102 -0.57312067
|
||||
2900 20456.181 115.03745 0 3903.2191 -20.118887
|
||||
2950 20779.493 55.321394 0 3903.3756 -0.26783079
|
||||
3000 20011.867 197.30216 0 3903.2035 -1.4704201
|
||||
3050 20741.875 62.208723 0 3903.2966 -7.5432815
|
||||
3100 21001.754 14.148298 0 3903.362 2.9676438
|
||||
3150 20244.086 154.44639 0 3903.3512 -1.9071213
|
||||
3200 20639.615 81.136426 0 3903.2873 1.4826467
|
||||
3250 20735.244 63.529571 0 3903.3895 2.1127055
|
||||
3300 20142.891 173.22282 0 3903.3878 4.7739415
|
||||
3350 19963.765 206.21899 0 3903.2126 5.5410771
|
||||
3400 16628.667 824.13627 0 3903.519 36.087673
|
||||
3450 19228.218 342.81569 0 3903.5968 3.1057274
|
||||
3500 19759.293 244.57876 0 3903.707 2.2339557
|
||||
3550 19853.21 227.06362 0 3903.584 -1.0882119
|
||||
3600 19673.516 260.64854 0 3903.8923 -10.63775
|
||||
3650 19619.238 270.5393 0 3903.7316 -6.3746003
|
||||
3700 20756.865 59.790243 0 3903.6542 -8.3015766
|
||||
3750 20265.025 150.47347 0 3903.2559 -5.7284695
|
||||
3800 20944.683 24.669276 0 3903.3142 -0.070552298
|
||||
3850 19344.831 320.59492 0 3902.971 13.040749
|
||||
3900 19978.209 203.00247 0 3902.6708 0.15638133
|
||||
3950 19864.118 224.19359 0 3902.734 0.453229
|
||||
4000 17606.216 642.71493 0 3903.1252 -12.656002
|
||||
4050 18017.895 566.54102 0 3903.1883 12.133906
|
||||
4100 20092.963 182.17593 0 3903.095 7.7445947
|
||||
4150 20555.337 96.395074 0 3902.939 -6.5429752
|
||||
4200 20709.781 67.869199 0 3903.0138 -2.8653003
|
||||
4250 18956.203 392.20748 0 3902.6155 -1.6249728
|
||||
4300 17816.204 603.72704 0 3903.0241 23.089239
|
||||
4350 18979.742 388.04678 0 3902.8138 3.2511108
|
||||
4400 20272.085 148.82367 0 3902.9135 1.9518268
|
||||
4450 18820.003 417.74789 0 3902.9337 6.3979299
|
||||
4500 19991.936 200.50131 0 3902.7117 3.5118553
|
||||
4550 20915.092 29.663898 0 3902.8291 -2.3174641
|
||||
4600 20690.37 71.125087 0 3902.6752 -12.008575
|
||||
4650 18893.76 404.50849 0 3903.3529 15.006184
|
||||
4700 18611.123 456.1263 0 3902.6306 -5.3574892
|
||||
4750 20497.821 106.5856 0 3902.4784 0.85039837
|
||||
4800 20803.214 50.120522 0 3902.5675 3.8610873
|
||||
4850 18849.598 411.72635 0 3902.3927 9.2029058
|
||||
4900 18121.714 546.68042 0 3902.5533 9.4522272
|
||||
4950 20377.499 128.99323 0 3902.6041 5.3825395
|
||||
5000 20686.114 72.039749 0 3902.8016 -5.706271
|
||||
5050 20180.449 165.51368 0 3902.634 -16.418461
|
||||
5100 20274.947 148.36657 0 3902.9864 -5.6668309
|
||||
5150 18042.324 560.74137 0 3901.9125 3.6791541
|
||||
5200 20794.666 52.204446 0 3903.0685 -1.4517721
|
||||
5250 19073.55 371.18834 0 3903.3272 -13.457439
|
||||
5300 20821.412 47.364313 0 3903.1813 2.258098
|
||||
5350 20583.073 91.271191 0 3902.9513 5.4323985
|
||||
5400 20490.967 108.41184 0 3903.0353 4.122905
|
||||
5450 18141.79 543.66874 0 3903.2594 -0.19951075
|
||||
5500 20274.012 148.55528 0 3903.002 5.0489974
|
||||
5550 17806.237 605.43454 0 3902.8858 43.80619
|
||||
5600 20999.825 14.341937 0 3903.1983 1.0879933
|
||||
5650 20930.929 27.025347 0 3903.1234 -7.0860209
|
||||
5700 20677.725 73.853093 0 3903.0614 2.6864775
|
||||
5750 20521.264 102.87509 0 3903.1092 2.6940548
|
||||
5800 20792.571 52.596021 0 3903.0721 1.2910217
|
||||
5850 20518.674 103.26595 0 3903.0204 -9.2547271
|
||||
5900 18417.885 491.66696 0 3902.3865 -12.049357
|
||||
5950 17243.837 709.37858 0 3902.6817 -6.2357188
|
||||
6000 20262.525 149.56918 0 3901.8885 -0.28964823
|
||||
6050 19883.554 219.14043 0 3901.2801 2.3071707
|
||||
6100 16548.178 838.47869 0 3902.956 -11.715644
|
||||
6150 19601.177 272.14674 0 3901.9944 -0.9008056
|
||||
6200 20499.796 106.2363 0 3902.4949 0.79071424
|
||||
6250 19601.106 272.50139 0 3902.3359 -1.9306693
|
||||
6300 17210.685 712.70535 0 3899.8692 4.8890923
|
||||
6350 19911.896 214.91041 0 3902.2985 12.691129
|
||||
6400 18834.642 411.87123 0 3899.7678 -1.9447856
|
||||
6450 20216.311 158.39781 0 3902.1591 2.6009109
|
||||
6500 20452.025 114.97122 0 3902.3832 0.14644416
|
||||
6550 19142.589 357.34097 0 3902.2649 2.8968485
|
||||
6600 20412.915 122.08784 0 3902.2573 3.1343105
|
||||
6650 17317.867 699.39994 0 3906.4123 42.25563
|
||||
6700 20479.771 109.8036 0 3902.3537 1.3520625
|
||||
6750 20306.902 142.12484 0 3902.6623 2.2032106
|
||||
6800 20755.367 58.994834 0 3902.5814 -0.90518094
|
||||
6850 20471.259 111.7197 0 3902.6936 1.5799331
|
||||
6900 20702.025 69.15032 0 3902.8586 9.3910371
|
||||
6950 20477.695 110.34414 0 3902.5099 1.8181164
|
||||
7000 20560.727 95.057704 0 3902.5998 -15.686006
|
||||
7050 20336.675 136.39386 0 3902.4448 1.3704327
|
||||
7100 20757.399 58.950153 0 3902.913 -6.4250981
|
||||
7150 20870.958 38.095649 0 3903.088 -4.1962169
|
||||
7200 20706.869 68.489134 0 3903.0944 2.8322659
|
||||
7250 20386.713 127.7432 0 3903.0604 6.0287391
|
||||
7300 18391.773 497.21001 0 3903.0939 19.202343
|
||||
7350 20178.898 166.4993 0 3903.3322 1.5682417
|
||||
7400 16858.704 781.78682 0 3903.7691 21.317514
|
||||
7450 17509.513 660.71963 0 3903.2221 -5.9456143
|
||||
7500 19974.601 204.20412 0 3903.2043 -0.69202711
|
||||
7550 20917.053 29.73415 0 3903.2626 -3.9962577
|
||||
7600 20923.518 28.482703 0 3903.2083 -1.9016251
|
||||
7650 20549.528 97.630612 0 3903.0987 3.5512257
|
||||
7700 20861.441 39.903885 0 3903.1337 2.4426264
|
||||
7750 18843.349 413.64461 0 3903.1537 2.677739
|
||||
7800 20616.054 85.214364 0 3903.0021 3.9639004
|
||||
7850 16478.851 851.93376 0 3903.5728 7.3763128
|
||||
7900 20312.115 141.35103 0 3902.8539 4.6707271
|
||||
7950 20389.623 127.16589 0 3903.0219 3.4414001
|
||||
8000 20452.117 115.30715 0 3902.7362 -1.0162528
|
||||
8050 20857.093 40.791886 0 3903.2164 -15.150068
|
||||
8100 19817.543 233.4997 0 3903.415 0.89346046
|
||||
8150 18649.521 449.9112 0 3903.5262 -0.40053588
|
||||
8200 19619.276 270.37616 0 3903.5754 5.5161492
|
||||
8250 20393.176 127.01336 0 3903.5275 2.122613
|
||||
8300 19145.912 358.00424 0 3903.5435 3.863924
|
||||
8350 19636.311 267.17226 0 3903.5262 -7.1496084
|
||||
8400 19086.332 368.86693 0 3903.3729 7.0968952
|
||||
8450 19494.416 292.89527 0 3902.9723 3.1750935
|
||||
8500 20041.919 191.77756 0 3903.244 0.95215503
|
||||
8550 20357.561 133.15478 0 3903.0736 -0.14020152
|
||||
8600 16998.797 756.07003 0 3903.9954 -16.724408
|
||||
8650 20853.26 41.386996 0 3903.1017 -3.2612965
|
||||
8700 20767.768 57.360884 0 3903.2438 1.1157649
|
||||
8750 20752.546 60.106518 0 3903.1705 0.39130547
|
||||
8800 20574.407 92.99798 0 3903.0734 0.61728166
|
||||
8850 20326.99 138.94203 0 3903.1995 -1.9434522
|
||||
8900 17408.108 679.53222 0 3903.2559 21.935371
|
||||
8950 20471.21 112.2721 0 3903.2368 1.8142747
|
||||
9000 19129.591 360.35257 0 3902.8694 4.5786395
|
||||
9050 20439.668 117.89541 0 3903.0191 2.5585685
|
||||
9100 20780.375 54.788664 0 3903.0062 3.8312459
|
||||
9150 19904.559 216.61504 0 3902.6445 12.150414
|
||||
9200 20961.295 21.52065 0 3903.2419 -0.2120699
|
||||
9250 19315.252 326.44175 0 3903.3402 -19.740867
|
||||
9300 20653.002 78.77764 0 3903.4076 -7.8068233
|
||||
9350 18961.572 391.20947 0 3902.6117 -12.660843
|
||||
9400 16262.179 892.67633 0 3904.191 22.2435
|
||||
9450 17064.394 743.33301 0 3903.406 36.139436
|
||||
9500 18075.588 555.06436 0 3902.3954 24.598176
|
||||
9550 20487.738 109.06287 0 3903.0884 2.6320759
|
||||
9600 20358.609 133.36993 0 3903.4828 0.76449113
|
||||
9650 19849.022 228.46312 0 3904.208 9.5547064
|
||||
9700 20448.112 116.8757 0 3903.5632 -1.0845697
|
||||
9750 20472.78 112.51661 0 3903.7722 -0.30676738
|
||||
9800 19491.99 293.35361 0 3902.9814 -20.10857
|
||||
9850 19895.603 218.42479 0 3902.7957 -0.18235641
|
||||
9900 19704.336 254.55068 0 3903.5019 14.553184
|
||||
9950 17689.462 627.9788 0 3903.805 4.9918088
|
||||
10000 20184.205 165.29396 0 3903.1097 2.9472364
|
||||
Loop time of 2.28393 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 37829.498 tau/day, 4378.414 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.052911 | 0.052911 | 0.052911 | 0.0 | 2.32
|
||||
Neigh | 0.056658 | 0.056658 | 0.056658 | 0.0 | 2.48
|
||||
Comm | 0.0087389 | 0.0087389 | 0.0087389 | 0.0 | 0.38
|
||||
Output | 0.0037996 | 0.0037996 | 0.0037996 | 0.0 | 0.17
|
||||
Modify | 2.1537 | 2.1537 | 2.1537 | 0.0 | 94.30
|
||||
Other | | 0.008147 | | | 0.36
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 113 ave 113 max 113 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 582 ave 582 max 582 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 582
|
||||
Ave neighs/atom = 7.1851852
|
||||
Neighbor list builds = 993
|
||||
Dangerous builds = 950
|
||||
Total wall time: 0:00:02
|
||||
329
examples/rigid/log.20Mar22.rigid.poems5.g++.4
Normal file
329
examples/rigid/log.20Mar22.rigid.poems5.g++.4
Normal file
@ -0,0 +1,329 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
Reading data file ...
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems file connected-bodies2.dat
|
||||
2 clusters, 9 bodies, 7 joints, 81 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix poems command:
|
||||
|
||||
@Article{Mukherjee08,
|
||||
author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
|
||||
title = {Substructured molecular dynamics using multibody dynamics algorithms},
|
||||
journal = {Intl.~J.~Non-linear Mechanics},
|
||||
year = 2008,
|
||||
volume = 43,
|
||||
pages = {1045--1055}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -2.7403788
|
||||
50 12774.759 1538.7382 0 3904.4344 18.086358
|
||||
100 19803.641 237.21132 0 3904.5523 -3.1528278
|
||||
150 20259.6 152.62072 0 3904.3985 -4.6173524
|
||||
200 20705.978 69.977039 0 3904.4174 9.0928122
|
||||
250 19552.211 283.50525 0 3904.285 15.670466
|
||||
300 19266.324 333.5792 0 3901.4169 7.2119197
|
||||
350 20738.325 63.738945 0 3904.1694 -23.03999
|
||||
400 20616.682 86.082444 0 3903.9864 -13.783584
|
||||
450 19831.326 230.13858 0 3902.6063 0.42074361
|
||||
500 20365.825 131.47271 0 3902.9217 0.69215592
|
||||
550 20794.102 52.163238 0 3902.9229 4.5895354
|
||||
600 20853.873 40.899172 0 3902.7275 2.3593042
|
||||
650 19255.802 336.29509 0 3902.1844 10.341742
|
||||
700 18526.969 471.02462 0 3901.9448 -0.61898691
|
||||
750 18960.662 391.26068 0 3902.4944 12.04731
|
||||
800 20142.432 172.05197 0 3902.1319 4.6838632
|
||||
850 19932.48 210.71175 0 3901.9118 3.4716031
|
||||
900 20243.528 153.13972 0 3901.9411 3.6490762
|
||||
950 20388.132 126.88722 0 3902.4671 -4.4518463
|
||||
1000 20076.333 184.61915 0 3902.4586 -2.272315
|
||||
1050 20859.506 39.696993 0 3902.5684 6.45166
|
||||
1100 15284.661 1072.1908 0 3902.6836 21.194042
|
||||
1150 19658.317 261.99809 0 3902.4272 -2.8744219
|
||||
1200 20767.681 56.717095 0 3902.5839 -34.817444
|
||||
1250 20625.583 82.586198 0 3902.1386 11.697328
|
||||
1300 20690.013 71.006478 0 3902.4903 -29.29278
|
||||
1350 20936.019 26.022786 0 3903.0634 1.0316025
|
||||
1400 19753.56 244.81784 0 3902.8844 6.7138497
|
||||
1450 15690.149 998.34213 0 3903.9252 48.124569
|
||||
1500 20234.455 155.92516 0 3903.0465 13.172207
|
||||
1550 20779.631 55.063019 0 3903.1428 -2.6390455
|
||||
1600 20642.753 80.233821 0 3902.9659 -2.4688431
|
||||
1650 18785.698 423.90364 0 3902.7365 -5.6466892
|
||||
1700 20965.076 20.760451 0 3903.182 -0.45366172
|
||||
1750 18935.412 396.95958 0 3903.5173 25.913174
|
||||
1800 20581.554 91.757912 0 3903.1567 3.8218442
|
||||
1850 20616.949 85.184789 0 3903.1382 4.1907933
|
||||
1900 16601.896 828.43849 0 3902.8638 -0.49468175
|
||||
1950 20175.564 166.52646 0 3902.7421 5.6035728
|
||||
2000 20262.525 150.28224 0 3902.6017 -1.1967705
|
||||
2050 20168.994 167.65314 0 3902.6521 -0.80723928
|
||||
2100 19810.955 232.96524 0 3901.6605 3.1936531
|
||||
2150 20667.232 75.645145 0 3902.9103 0.54812734
|
||||
2200 19863.772 224.34646 0 3902.8228 7.9294465
|
||||
2250 18808.943 419.2084 0 3902.3461 14.344526
|
||||
2300 20573.665 92.761842 0 3902.6999 -6.7671703
|
||||
2350 19075.104 369.95414 0 3902.3809 -9.5353568
|
||||
2400 20273.873 148.53775 0 3902.9586 -1.93796
|
||||
2450 20087.769 182.30216 0 3902.2593 2.131796
|
||||
2500 20711.602 67.530554 0 3903.0124 2.6280244
|
||||
2550 19971.224 204.75926 0 3903.134 3.1760522
|
||||
2600 20620.084 85.027145 0 3903.5612 -0.92888063
|
||||
2650 19737.546 248.65474 0 3903.7559 -3.3218688
|
||||
2700 20650.724 79.522243 0 3903.7303 -7.5918025
|
||||
2750 19863.245 225.2505 0 3903.6292 9.2140221
|
||||
2800 18992.457 386.73547 0 3903.8572 2.6244537
|
||||
2850 18703.899 440.48356 0 3904.1685 14.561348
|
||||
2900 17939.805 581.74599 0 3903.932 -8.0863089
|
||||
2950 20867.516 39.38186 0 3903.7367 3.0985423
|
||||
3000 19767.994 242.8847 0 3903.6243 1.5943109
|
||||
3050 20397.448 126.31591 0 3903.6212 -0.14982775
|
||||
3100 20978.114 19.126395 0 3903.9623 -9.6797253
|
||||
3150 18303.556 513.8514 0 3903.3989 4.5940322
|
||||
3200 19156.505 356.46608 0 3903.9671 10.071308
|
||||
3250 17484.205 666.52199 0 3904.3377 -4.1641768
|
||||
3300 18069.94 557.75947 0 3904.0447 11.868707
|
||||
3350 20855.645 41.964632 0 3904.1212 5.4186293
|
||||
3400 18011.986 568.76255 0 3904.3155 25.262783
|
||||
3450 18669.69 446.92755 0 3904.2776 -4.194499
|
||||
3500 20248.799 154.22147 0 3903.9991 3.9211572
|
||||
3550 20226.024 158.64726 0 3904.2072 1.5299114
|
||||
3600 20267.02 151.25631 0 3904.4082 -8.9821729
|
||||
3650 20522.946 103.65382 0 3904.1994 -14.433796
|
||||
3700 20892.319 35.294614 0 3904.2426 -21.264596
|
||||
3750 19942.202 211.02993 0 3904.0304 -1.6428817
|
||||
3800 20421.678 122.08118 0 3903.8734 1.7137935
|
||||
3850 17899.53 588.82593 0 3903.5536 -24.450276
|
||||
3900 20721.119 66.486999 0 3903.7312 -7.1772088
|
||||
3950 20946.484 24.799445 0 3903.778 -0.4028037
|
||||
4000 20985.362 17.608355 0 3903.7865 4.7522266
|
||||
4050 19969.779 205.46466 0 3903.5719 18.941639
|
||||
4100 20479.578 110.56561 0 3903.08 2.3715952
|
||||
4150 18110.701 549.53348 0 3903.367 1.133321
|
||||
4200 19321.098 325.58216 0 3903.5634 -3.7574942
|
||||
4250 20734.436 63.87616 0 3903.5865 0.48350623
|
||||
4300 19446.823 302.1727 0 3903.4362 4.0462392
|
||||
4350 20494.669 108.1918 0 3903.501 2.9789077
|
||||
4400 20379.244 129.61413 0 3903.5482 4.0881089
|
||||
4450 19710.564 253.4251 0 3903.5295 5.3334683
|
||||
4500 20744.753 61.785082 0 3903.406 4.0015409
|
||||
4550 19948.024 208.76984 0 3902.8484 2.705423
|
||||
4600 18367.368 502.69569 0 3904.0602 21.476471
|
||||
4650 20559.367 96.133242 0 3903.4234 2.2549454
|
||||
4700 20940.135 25.547808 0 3903.3505 -8.9042666
|
||||
4750 20128.703 175.82088 0 3903.3584 -8.1450176
|
||||
4800 20632.27 82.543887 0 3903.3347 -0.55649542
|
||||
4850 19864.539 224.63792 0 3903.2563 7.1553461
|
||||
4900 19332.037 323.15561 0 3903.1625 17.020214
|
||||
4950 19055.575 373.68069 0 3902.4908 10.149457
|
||||
5000 20219.484 159.21383 0 3903.5627 3.1806346
|
||||
5050 17557.761 652.32864 0 3903.7659 10.733736
|
||||
5100 20615.337 85.795304 0 3903.4503 -3.6035636
|
||||
5150 20759.853 59.155843 0 3903.573 2.0152286
|
||||
5200 20082.007 184.39375 0 3903.2839 -5.3745109
|
||||
5250 18689.521 442.59842 0 3903.6208 -9.8911164
|
||||
5300 20038.496 192.34221 0 3903.1749 -2.1437039
|
||||
5350 19897.455 218.70142 0 3903.4154 0.64582116
|
||||
5400 18732.385 434.21543 0 3903.1755 12.98676
|
||||
5450 19831.487 230.79099 0 3903.2886 11.439958
|
||||
5500 20079.89 184.6953 0 3903.1935 4.0906279
|
||||
5550 20453.497 115.47128 0 3903.1559 7.8844436
|
||||
5600 16673.041 815.52661 0 3903.1267 -20.17797
|
||||
5650 19691.378 256.6412 0 3903.1928 3.7103317
|
||||
5700 20345.743 135.29997 0 3903.0302 5.6373816
|
||||
5750 20769.613 56.906603 0 3903.1312 -17.564762
|
||||
5800 20713.369 67.38314 0 3903.1922 -5.340631
|
||||
5850 20799.947 51.348865 0 3903.1909 -2.7827653
|
||||
5900 19581.933 273.51588 0 3899.7997 12.347375
|
||||
5950 20444.438 116.909 0 3902.9161 -0.74896654
|
||||
6000 18970.948 389.99664 0 3903.1352 26.642912
|
||||
6050 19414.753 307.13217 0 3902.4568 25.86316
|
||||
6100 20780.042 54.586474 0 3902.7424 1.5387425
|
||||
6150 20885.872 35.091585 0 3902.8456 -8.251884
|
||||
6200 19825.81 231.40943 0 3902.8558 6.7196589
|
||||
6250 20578.278 92.255994 0 3903.0481 -5.9647091
|
||||
6300 20093.43 181.8699 0 3902.8754 -9.9906069
|
||||
6350 20605.294 87.180289 0 3902.9755 -3.5643876
|
||||
6400 19737.257 247.84828 0 3902.8958 -4.2783347
|
||||
6450 19884.717 220.81633 0 3903.1714 3.8758905
|
||||
6500 18719.372 436.94802 0 3903.4984 1.7865904
|
||||
6550 20096.883 181.63346 0 3903.2784 2.395512
|
||||
6600 20888.673 35.003062 0 3903.2758 2.7728947
|
||||
6650 20437.85 118.16373 0 3902.9507 8.1456757
|
||||
6700 19241.051 339.73065 0 3902.8882 13.740454
|
||||
6750 20407.542 123.94326 0 3903.1177 7.6285942
|
||||
6800 20536.785 99.976706 0 3903.0851 8.3496632
|
||||
6850 20625.328 83.579677 0 3903.0849 6.5074992
|
||||
6900 20705.37 68.944625 0 3903.2724 3.1905177
|
||||
6950 18872.424 408.67134 0 3903.5647 6.2638845
|
||||
7000 20072.762 186.18051 0 3903.3586 -22.780407
|
||||
7050 20461.879 114.07495 0 3903.3117 -11.495523
|
||||
7100 19811.566 234.50237 0 3903.3108 1.1212695
|
||||
7150 20742.918 61.884088 0 3903.1651 -3.7907508
|
||||
7200 20911.192 30.599903 0 3903.0429 -7.0262304
|
||||
7250 20879.755 36.30274 0 3902.9241 -5.8018787
|
||||
7300 20682.32 72.703261 0 3902.7626 -3.3446789
|
||||
7350 19401.046 309.70672 0 3902.493 3.4836528
|
||||
7400 20220.542 157.83897 0 3902.3838 2.3400031
|
||||
7450 17691.193 625.47764 0 3901.6244 25.239568
|
||||
7500 19745.294 245.02566 0 3901.5615 5.3622843
|
||||
7550 19685.719 256.70983 0 3902.2133 3.4560563
|
||||
7600 18830.192 415.10021 0 3902.1727 -0.10282681
|
||||
7650 19613.136 270.18979 0 3902.2521 8.2241536
|
||||
7700 20989.015 15.636879 0 3902.4915 1.2955204
|
||||
7750 20301.583 142.90625 0 3902.4586 0.12548373
|
||||
7800 18360.147 502.50342 0 3902.5307 17.117272
|
||||
7850 20796.478 51.032537 0 3902.2321 -3.0993883
|
||||
7900 20284.267 145.64296 0 3901.9887 -1.2682383
|
||||
7950 20280.983 146.13471 0 3901.8723 3.5999841
|
||||
8000 20915.869 28.730821 0 3902.0399 2.4987291
|
||||
8050 20745.162 60.19981 0 3901.8964 4.0643481
|
||||
8100 20509.039 103.70462 0 3901.6748 1.0771863
|
||||
8150 20212.97 158.64893 0 3901.7916 3.0000215
|
||||
8200 20323.463 138.25912 0 3901.8634 -1.2802945
|
||||
8250 19997.284 198.37183 0 3901.5727 -2.6431964
|
||||
8300 20138.402 171.75824 0 3901.092 1.7669897
|
||||
8350 20367.568 130.22531 0 3901.9972 -1.2153731
|
||||
8400 19945.534 208.35675 0 3901.9741 1.6021151
|
||||
8450 20112.534 177.18642 0 3901.7298 2.2413008
|
||||
8500 20686.7 71.116816 0 3901.9873 2.2888545
|
||||
8550 18081.94 553.83586 0 3902.3432 7.8257937
|
||||
8600 18320.081 505.67086 0 3898.2784 16.554878
|
||||
8650 20235.305 154.43021 0 3901.709 3.1740823
|
||||
8700 20355.413 132.22512 0 3901.746 4.3436482
|
||||
8750 20087.188 182.11349 0 3901.9631 10.422134
|
||||
8800 20400.795 124.09819 0 3902.0232 2.1179177
|
||||
8850 20678.731 72.825797 0 3902.2204 -3.4491441
|
||||
8900 20372.643 129.5072 0 3902.2189 -8.2166415
|
||||
8950 20851.731 40.899364 0 3902.331 -5.8382839
|
||||
9000 20318.076 139.61775 0 3902.2243 -4.1960802
|
||||
9050 16879.415 776.53739 0 3902.3549 -14.429475
|
||||
9100 19135.149 358.68223 0 3902.2284 -15.50479
|
||||
9150 20689.556 70.939656 0 3902.339 -2.9876179
|
||||
9200 19949.801 207.54882 0 3901.9564 6.4259245
|
||||
9250 20207.027 160.2813 0 3902.3233 1.7402195
|
||||
9300 20030.005 192.99466 0 3902.2548 5.300728
|
||||
9350 19795.291 236.24003 0 3902.0347 5.8677745
|
||||
9400 18232.093 526.18752 0 3902.501 19.344893
|
||||
9450 18789.641 422.30568 0 3901.8687 -7.5185247
|
||||
9500 16332.599 874.10423 0 3898.6597 16.241378
|
||||
9550 18572.572 462.19972 0 3901.5649 -10.777359
|
||||
9600 19859.645 223.32209 0 3901.0341 0.89631957
|
||||
9650 19092.741 365.35768 0 3901.0504 6.7830005
|
||||
9700 18391.154 495.72792 0 3901.4972 6.0683847
|
||||
9750 17790.092 608.60997 0 3903.0714 8.2090184
|
||||
9800 17681.783 628.99951 0 3903.4038 14.231747
|
||||
9850 17804.412 605.54067 0 3902.654 22.308453
|
||||
9900 19134.472 359.37911 0 3902.7999 8.5633158
|
||||
9950 20099.055 180.28604 0 3902.3332 4.7905855
|
||||
10000 20035.447 192.30744 0 3902.5754 1.8299201
|
||||
Loop time of 2.34062 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 36913.309 tau/day, 4272.374 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0052865 | 0.014915 | 0.039366 | 11.6 | 0.64
|
||||
Neigh | 0.0080708 | 0.016504 | 0.03345 | 7.7 | 0.71
|
||||
Comm | 0.1357 | 0.14237 | 0.15111 | 1.5 | 6.08
|
||||
Output | 0.0033429 | 0.0037922 | 0.0050931 | 1.2 | 0.16
|
||||
Modify | 2.1033 | 2.1433 | 2.1609 | 1.6 | 91.57
|
||||
Other | | 0.01973 | | | 0.84
|
||||
|
||||
Nlocal: 20.25 ave 36 max 0 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 35.25 ave 47 max 24 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 137.5 ave 252 max 0 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 550
|
||||
Ave neighs/atom = 6.7901235
|
||||
Neighbor list builds = 994
|
||||
Dangerous builds = 956
|
||||
Total wall time: 0:00:02
|
||||
@ -1,338 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.292 | 3.292 | 3.292 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045743
|
||||
850 17821.483 711.53827 0 3681.7854 7.4384277
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19375 0 3681.3037 11.787983
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184717
|
||||
1150 20849.582 206.01695 0 3680.9472 -0.86699149
|
||||
1200 21815.003 45.317414 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064078
|
||||
1300 20780.781 217.36506 0 3680.8286 6.0538616
|
||||
1350 20558.971 254.36482 0 3680.8601 -3.6773952
|
||||
1400 21485.029 99.812921 0 3680.6511 -16.185473
|
||||
1450 21771.107 52.15961 0 3680.6775 -2.4756673
|
||||
1500 21520.948 93.503927 0 3680.3286 2.1023576
|
||||
1550 21351.418 121.68137 0 3680.2511 5.5159947
|
||||
1600 20778.805 216.92177 0 3680.0559 15.089188
|
||||
1650 21477.638 100.21836 0 3679.8247 -1.1045746
|
||||
1700 18501.339 596.47914 0 3680.0357 -15.679679
|
||||
1750 18563.642 587.34785 0 3681.2882 33.532209
|
||||
1800 19110.185 494.8234 0 3679.8543 18.024046
|
||||
1850 21364.191 119.23545 0 3679.9339 2.5291103
|
||||
1900 20146.626 322.14867 0 3679.9197 5.7313218
|
||||
1950 20692.672 231.25325 0 3680.0319 4.2977763
|
||||
2000 20943.904 189.11235 0 3679.7629 -22.645121
|
||||
2050 19668.057 401.82994 0 3679.8394 3.6251916
|
||||
2100 20280.442 299.76155 0 3679.8353 7.4807949
|
||||
2150 19181.86 483.522 0 3680.4987 22.620507
|
||||
2200 21300.161 130.70534 0 3680.7322 4.7102665
|
||||
2250 20486.943 266.63931 0 3681.1299 -8.6456512
|
||||
2300 18653.122 572.24819 0 3681.1018 -5.2637122
|
||||
2350 21513.523 95.614901 0 3681.2021 -9.3621767
|
||||
2400 21466.272 103.56446 0 3681.2765 -29.561368
|
||||
2450 20100.105 332.27123 0 3682.2887 35.744287
|
||||
2500 20764.395 221.6677 0 3682.4001 -12.468906
|
||||
2550 20435.699 276.31055 0 3682.2603 -22.413697
|
||||
2600 21466.467 104.53618 0 3682.2807 -10.078508
|
||||
2650 20814.737 213.23892 0 3682.3617 5.1390411
|
||||
2700 18565.761 588.3578 0 3682.6513 22.27664
|
||||
2750 20772.36 220.1607 0 3682.2206 -7.9448198
|
||||
2800 21018.563 179.10058 0 3682.1945 -7.0717829
|
||||
2850 16789.412 884.21472 0 3682.4501 33.279015
|
||||
2900 19304.363 464.75282 0 3682.1466 7.947554
|
||||
2950 20513.758 263.07578 0 3682.0355 2.2361434
|
||||
3000 20617.309 245.95251 0 3682.1706 -0.75213689
|
||||
3050 18567.52 587.90473 0 3682.4914 -4.0112006
|
||||
3100 18696.577 566.20617 0 3682.3023 -1.4814167
|
||||
3150 19864.606 371.56078 0 3682.3284 8.9362836
|
||||
3200 18902.643 532.04614 0 3682.4867 0.76630303
|
||||
3250 21110.454 163.86212 0 3682.271 -1.6253894
|
||||
3300 19369.939 454.05833 0 3682.3816 4.9066544
|
||||
3350 19082.603 501.69905 0 3682.133 3.5982292
|
||||
3400 19527.779 426.918 0 3681.5478 6.9612143
|
||||
3450 19892.953 366.19989 0 3681.6921 3.0050426
|
||||
3500 19708.981 396.84552 0 3681.6756 7.0757635
|
||||
3550 20256.096 306.23937 0 3682.2554 -1.752138
|
||||
3600 21289.889 133.93823 0 3682.253 -3.7462615
|
||||
3650 18333.877 627.18028 0 3682.8264 -15.276791
|
||||
3700 19829.133 377.33753 0 3682.1931 -6.269648
|
||||
3750 20771.635 220.07171 0 3682.0109 -28.479036
|
||||
3800 18373.813 619.79253 0 3682.0947 29.594781
|
||||
3850 19320.99 461.92786 0 3682.0928 -5.3212101
|
||||
3900 16119.825 995.68064 0 3682.3182 -8.4683118
|
||||
3950 15556.948 1091.3655 0 3684.1902 20.98273
|
||||
4000 20000.464 348.24891 0 3681.6596 7.1589745
|
||||
4050 18870.219 536.59924 0 3681.6358 -3.7997025
|
||||
4100 19889.518 367.49253 0 3682.4122 -14.091266
|
||||
4150 15789.623 1051.3399 0 3682.9438 -4.4152389
|
||||
4200 20548.889 256.83493 0 3681.6498 0.92234153
|
||||
4250 20681.925 235.46113 0 3682.4487 -11.515773
|
||||
4300 19330.404 460.80975 0 3682.5437 -22.351775
|
||||
4350 19369.443 453.35405 0 3681.5945 29.418242
|
||||
4400 20762.165 222.24133 0 3682.6021 2.6627047
|
||||
4450 19984.657 350.71294 0 3681.4891 28.88731
|
||||
4500 21167.58 154.25344 0 3682.1834 -3.0784322
|
||||
4550 18133.576 660.73671 0 3682.9995 2.5305835
|
||||
4600 19935.069 360.36826 0 3682.8798 2.4575034
|
||||
4650 21413.76 113.86464 0 3682.8246 -5.1271547
|
||||
4700 21716.333 63.609419 0 3682.9982 -2.4708049
|
||||
4750 21352.947 124.36961 0 3683.1941 -0.29026265
|
||||
4800 19043.788 508.8617 0 3682.8264 14.797006
|
||||
4850 20516.121 263.78758 0 3683.1411 7.1348281
|
||||
4900 20624.5 245.81827 0 3683.235 0.34708051
|
||||
4950 20317.197 296.68937 0 3682.8889 -0.55065946
|
||||
5000 18346.865 625.37246 0 3683.1832 7.3371413
|
||||
5050 18867.53 538.49153 0 3683.0799 1.9249866
|
||||
5100 18790.276 551.17224 0 3682.885 2.2333017
|
||||
5150 20241.365 311.84683 0 3685.4076 -3.998004
|
||||
5200 17685.058 739.76418 0 3687.2739 3.2835025
|
||||
5250 18496.626 604.58166 0 3687.3526 -10.185776
|
||||
5300 18420.042 617.82026 0 3687.8273 -16.392458
|
||||
5350 18767.338 559.0349 0 3686.9246 4.5320767
|
||||
5400 20423.245 284.90517 0 3688.7794 -8.6356656
|
||||
5450 21080.398 176.18494 0 3689.5846 -16.450038
|
||||
5500 16684.424 909.12643 0 3689.8637 49.94555
|
||||
5550 20132.31 335.03663 0 3690.4216 -16.018038
|
||||
5600 20430.923 285.17562 0 3690.3295 -5.0773675
|
||||
5650 20479.943 276.55962 0 3689.8834 5.4334564
|
||||
5700 20061.532 345.95553 0 3689.5441 -16.230658
|
||||
5750 20523.759 268.92217 0 3689.5487 -4.4128812
|
||||
5800 18900.356 537.65462 0 3687.7139 13.605549
|
||||
5850 20280.502 310.27193 0 3690.3556 -4.7884959
|
||||
5900 19050.26 515.66087 0 3690.7042 7.8864722
|
||||
5950 19566.917 430.2997 0 3691.4525 31.715268
|
||||
6000 18878.118 544.75449 0 3691.1076 -4.2415329
|
||||
6050 19308.682 471.70734 0 3689.821 -10.561614
|
||||
6100 18776.194 560.04764 0 3689.4133 -7.7286747
|
||||
6150 21475.064 110.1508 0 3689.3281 -3.6506391
|
||||
6200 19975 360.82675 0 3689.9934 10.282021
|
||||
6250 21396.341 123.5341 0 3689.5909 -5.7215163
|
||||
6300 18533.423 600.87422 0 3689.778 15.408027
|
||||
6350 20653.152 247.19253 0 3689.3846 8.5607784
|
||||
6400 19716.537 403.41487 0 3689.5044 13.165575
|
||||
6450 21120.66 168.79838 0 3688.9084 -0.50382728
|
||||
6500 19700.345 404.7155 0 3688.1064 13.941375
|
||||
6550 10818.393 1892.037 0 3695.1025 38.423155
|
||||
6600 18684.478 574.84755 0 3688.9273 5.9176985
|
||||
6650 19219.732 486.04269 0 3689.3314 18.287659
|
||||
6700 20058.587 344.88255 0 3687.9804 6.5372086
|
||||
6750 21279.318 142.77333 0 3689.3264 2.498188
|
||||
6800 20671.545 244.25024 0 3689.5078 -4.1356416
|
||||
6850 21203.598 155.82001 0 3689.753 -0.0083061182
|
||||
6900 21699.344 73.301497 0 3689.8588 -8.0309898
|
||||
6950 20951.212 197.19403 0 3689.0627 0.76668303
|
||||
7000 20166.275 329.02869 0 3690.0746 2.0083318
|
||||
7050 21554.944 97.465792 0 3689.9564 -3.2420086
|
||||
7100 20817.494 220.25476 0 3689.8372 0.17206182
|
||||
7150 21481.11 109.84029 0 3690.0253 -3.6814741
|
||||
7200 21266.824 145.53099 0 3690.0016 -2.060543
|
||||
7250 19434.684 450.81331 0 3689.9273 9.4822765
|
||||
7300 21246.525 148.96573 0 3690.0532 3.3208839
|
||||
7350 19749.269 398.60049 0 3690.1454 1.0929662
|
||||
7400 20354.792 297.70261 0 3690.168 1.547159
|
||||
7450 19996.859 357.16723 0 3689.977 -0.68412025
|
||||
7500 20179.628 326.53243 0 3689.8038 -2.4805507
|
||||
7550 18765.184 561.65039 0 3689.1811 -1.7976428
|
||||
7600 19457.496 447.04428 0 3689.9603 -1.9055522
|
||||
7650 18206.823 655.57276 0 3690.0433 1.2797964
|
||||
7700 19152.344 497.77422 0 3689.8315 18.145069
|
||||
7750 21387.484 125.48654 0 3690.0673 -2.9915772
|
||||
7800 18127.052 668.61425 0 3689.7896 9.044869
|
||||
7850 21419.557 120.08889 0 3690.015 6.2651717
|
||||
7900 21817.182 53.739819 0 3689.9368 -4.2387416
|
||||
7950 18215.195 654.15494 0 3690.0208 -54.628049
|
||||
8000 21523.503 102.58018 0 3689.8307 -4.84236
|
||||
8050 20720.799 236.28689 0 3689.7535 -9.3725225
|
||||
8100 21196.483 157.3232 0 3690.0704 -7.7222497
|
||||
8150 20869.667 211.65308 0 3689.9309 -6.8438295
|
||||
8200 17790.052 725.72497 0 3690.7336 -25.697688
|
||||
8250 19634.94 417.71929 0 3690.2094 8.861604
|
||||
8300 19135.784 500.92443 0 3690.2218 -3.1245167
|
||||
8350 20191.718 324.93312 0 3690.2195 6.5736107
|
||||
8400 20695.239 241.02378 0 3690.2302 -14.592221
|
||||
8450 21793.857 57.609525 0 3689.9191 -11.509747
|
||||
8500 21271.088 144.43102 0 3689.6124 -0.091587085
|
||||
8550 20064.337 345.21754 0 3689.2737 9.5058471
|
||||
8600 20282.86 308.2307 0 3688.7074 2.265529
|
||||
8650 21223.055 151.24306 0 3688.419 1.7296834
|
||||
8700 18875.342 542.42055 0 3688.3108 6.367148
|
||||
8750 20922.65 201.55122 0 3688.6595 3.4208578
|
||||
8800 21406.54 120.8539 0 3688.6106 1.8253729
|
||||
8850 19868.524 377.05623 0 3688.477 16.327796
|
||||
8900 20025.322 348.94892 0 3686.5025 17.063406
|
||||
8950 21224.374 151.3567 0 3688.7524 -0.11028753
|
||||
9000 21318.309 135.862 0 3688.9135 -0.50826819
|
||||
9050 17538.618 768.00136 0 3691.1043 37.978645
|
||||
9100 21247.861 147.84641 0 3689.1566 -6.7773259
|
||||
9150 18455.677 613.08767 0 3689.0339 -3.4844751
|
||||
9200 19486.859 441.03829 0 3688.8482 -18.602827
|
||||
9250 21774.926 59.710446 0 3688.8648 -13.379919
|
||||
9300 17628.877 750.72321 0 3688.8694 27.797974
|
||||
9350 19827.334 383.85708 0 3688.4128 6.5459021
|
||||
9400 20020.126 351.61742 0 3688.3051 -14.332562
|
||||
9450 21596.338 88.904175 0 3688.2939 1.5779716
|
||||
9500 18981.418 524.60141 0 3688.1711 5.4352409
|
||||
9550 18652.616 579.05144 0 3687.8208 25.600729
|
||||
9600 21198.037 155.23097 0 3688.2371 -3.3586596
|
||||
9650 19958.317 361.32544 0 3687.7115 4.2910178
|
||||
9700 19129.101 499.5993 0 3687.7828 13.267102
|
||||
9750 21913.967 35.689587 0 3688.0174 -7.3222905
|
||||
9800 21314.694 135.43794 0 3687.8869 -9.5613518
|
||||
9850 20899.743 204.82802 0 3688.1185 -2.6321428
|
||||
9900 20288.244 306.5013 0 3687.8753 3.6196618
|
||||
9950 19271.015 475.88527 0 3687.7211 -1.8196764
|
||||
10000 21122.24 167.82714 0 3688.2005 -3.8464842
|
||||
Loop time of 6.61148 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 13068.179 tau/day, 1512.521 timesteps/s
|
||||
97.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14595 | 0.14595 | 0.14595 | 0.0 | 2.21
|
||||
Neigh | 0.10704 | 0.10704 | 0.10704 | 0.0 | 1.62
|
||||
Comm | 0.013317 | 0.013317 | 0.013317 | 0.0 | 0.20
|
||||
Output | 0.0047956 | 0.0047956 | 0.0047956 | 0.0 | 0.07
|
||||
Modify | 6.3318 | 6.3318 | 6.3318 | 0.0 | 95.77
|
||||
Other | | 0.008603 | | | 0.13
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 95 ave 95 max 95 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 744 ave 744 max 744 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 744
|
||||
Ave neighs/atom = 9.18519
|
||||
Neighbor list builds = 992
|
||||
Dangerous builds = 941
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:06
|
||||
@ -1,338 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.263 | 3.357 | 3.638 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045743
|
||||
850 17821.483 711.53827 0 3681.7854 7.4384276
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19375 0 3681.3037 11.787983
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184718
|
||||
1150 20849.582 206.01695 0 3680.9472 -0.8669916
|
||||
1200 21815.003 45.317417 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064076
|
||||
1300 20780.781 217.36504 0 3680.8286 6.0538619
|
||||
1350 20558.972 254.3648 0 3680.8601 -3.6773987
|
||||
1400 21485.029 99.812949 0 3680.6511 -16.185471
|
||||
1450 21771.108 52.15959 0 3680.6775 -2.4756681
|
||||
1500 21520.948 93.503949 0 3680.3286 2.1023578
|
||||
1550 21351.418 121.6814 0 3680.2511 5.5159978
|
||||
1600 20778.805 216.92171 0 3680.0559 15.089182
|
||||
1650 21477.639 100.2182 0 3679.8247 -1.1045944
|
||||
1700 18501.343 596.47853 0 3680.0357 -15.67963
|
||||
1750 18563.643 587.34767 0 3681.2882 33.532167
|
||||
1800 19110.19 494.82264 0 3679.8543 18.024034
|
||||
1850 21364.196 119.23454 0 3679.9339 2.5291491
|
||||
1900 20146.643 322.14595 0 3679.9197 5.731152
|
||||
1950 20692.67 231.25357 0 3680.0319 4.2977641
|
||||
2000 20943.904 189.11223 0 3679.763 -22.645645
|
||||
2050 19668.152 401.81407 0 3679.8394 3.6255896
|
||||
2100 20280.572 299.73976 0 3679.8351 7.4809355
|
||||
2150 19182.121 483.47905 0 3680.4992 22.615309
|
||||
2200 21299.76 130.77281 0 3680.7327 4.7114154
|
||||
2250 20487.784 266.4995 0 3681.1302 -8.6406776
|
||||
2300 18655.125 571.91487 0 3681.1023 -5.2671669
|
||||
2350 21512.614 95.766913 0 3681.2025 -9.3523428
|
||||
2400 21467.773 103.31519 0 3681.2773 -29.600307
|
||||
2450 20096.937 332.80159 0 3682.2911 35.890912
|
||||
2500 20761.446 222.16118 0 3682.4022 -12.528127
|
||||
2550 20409.6 280.67234 0 3682.2723 -22.277373
|
||||
2600 21469.964 103.95529 0 3682.2826 -10.038267
|
||||
2650 20708.138 231.00516 0 3682.3615 5.3659502
|
||||
2700 18584.743 585.07862 0 3682.5357 21.785261
|
||||
2750 20503.019 264.91491 0 3682.0847 -4.5583917
|
||||
2800 20584.075 251.44664 0 3682.1258 -6.5084595
|
||||
2850 17277.076 802.33356 0 3681.8462 15.519513
|
||||
2900 19392.956 449.92915 0 3682.0885 -4.3829957
|
||||
2950 18371.786 620.29835 0 3682.2626 7.2117592
|
||||
3000 20412.015 280.25302 0 3682.2555 0.32492606
|
||||
3050 20858.248 205.65269 0 3682.0273 4.5055715
|
||||
3100 21561.094 88.438447 0 3681.9541 -3.7523733
|
||||
3150 15471.278 1103.4497 0 3681.9961 -14.576367
|
||||
3200 15386.973 1117.8815 0 3682.377 15.051163
|
||||
3250 19741.037 392.04755 0 3682.2204 -2.6610995
|
||||
3300 20870.191 203.58229 0 3681.9475 -4.7795545
|
||||
3350 16648.228 907.66571 0 3682.3704 -8.9242511
|
||||
3400 20104.016 331.58603 0 3682.2554 6.4783858
|
||||
3450 21421.316 112.28228 0 3682.5015 -8.3484987
|
||||
3500 19284.533 467.80739 0 3681.8962 -12.835452
|
||||
3550 20160.125 322.4476 0 3682.4684 1.6574827
|
||||
3600 16682.415 902.73752 0 3683.14 22.383296
|
||||
3650 16762.19 890.14636 0 3683.8446 16.119412
|
||||
3700 17858.568 707.37212 0 3683.8 -1.6582504
|
||||
3750 20029.881 345.15986 0 3683.4733 -3.1415889
|
||||
3800 20734 227.99158 0 3683.6582 -7.9580418
|
||||
3850 20741.089 226.39408 0 3683.2423 8.3055765
|
||||
3900 18671.251 571.42296 0 3683.2981 -3.7468858
|
||||
3950 19547.209 423.14256 0 3681.0108 5.8312279
|
||||
4000 19739.799 393.58799 0 3683.5544 18.604884
|
||||
4050 20014.121 347.8176 0 3683.5044 9.93387
|
||||
4100 20503.654 266.08691 0 3683.3626 8.1304118
|
||||
4150 18309.702 632.29807 0 3683.9151 -0.0021480359
|
||||
4200 20509.423 265.60353 0 3683.8408 -2.1658857
|
||||
4250 21805.541 50.325935 0 3684.5828 1.082842
|
||||
4300 21420.551 114.90431 0 3684.9962 -1.7985998
|
||||
4350 20256.928 308.74187 0 3684.8966 -11.669472
|
||||
4400 21633.488 79.629274 0 3685.2106 -0.96131785
|
||||
4450 20793.327 219.66955 0 3685.2241 1.3752349
|
||||
4500 18719.484 564.86754 0 3684.7816 2.6308699
|
||||
4550 20966.335 190.68308 0 3685.0722 -18.587627
|
||||
4600 19428.962 446.59618 0 3684.7565 -4.4051672
|
||||
4650 18408.956 616.85009 0 3685.0095 2.777272
|
||||
4700 19215.779 482.57562 0 3685.2054 19.441016
|
||||
4750 20155.927 326.13401 0 3685.4553 6.1734993
|
||||
4800 20918.085 199.31832 0 3685.6659 3.4407437
|
||||
4850 20236.958 312.07276 0 3684.899 3.2612893
|
||||
4900 21419.89 115.36879 0 3685.3505 -4.675951
|
||||
4950 19707.901 401.14828 0 3685.7985 -10.730734
|
||||
5000 19407.201 450.64394 0 3685.1775 17.518981
|
||||
5050 21527.598 97.655186 0 3685.5882 -9.2294707
|
||||
5100 21581.933 88.595517 0 3685.5843 -20.669485
|
||||
5150 21161.214 158.48503 0 3685.3541 -2.7587502
|
||||
5200 21166.679 157.24762 0 3685.0275 -18.180044
|
||||
5250 20909.576 200.23507 0 3685.1644 -16.617303
|
||||
5300 21911.746 33.236563 0 3685.1942 -5.8313967
|
||||
5350 20857.303 208.87453 0 3685.0916 12.176312
|
||||
5400 20958.96 191.96694 0 3685.1269 3.6116429
|
||||
5450 20433.179 279.61178 0 3685.1415 13.324529
|
||||
5500 19604.675 416.88499 0 3684.3308 21.536484
|
||||
5550 18171.145 655.92915 0 3684.4534 -9.2269804
|
||||
5600 19799.907 385.12116 0 3685.1056 22.202165
|
||||
5650 19711.882 399.30581 0 3684.6194 15.93063
|
||||
5700 17908.833 699.52405 0 3684.3295 0.35530356
|
||||
5750 18606.518 583.538 0 3684.6243 -4.4540843
|
||||
5800 21814.053 48.974627 0 3684.6501 -1.5206358
|
||||
5850 18029.107 679.9357 0 3684.7868 12.137677
|
||||
5900 21090.739 169.64502 0 3684.7682 -1.5051545
|
||||
5950 21086.26 170.29075 0 3684.6674 -2.8164474
|
||||
6000 21285.771 136.95608 0 3684.5846 -26.582739
|
||||
6050 21203.994 150.87822 0 3684.8772 -2.6617226
|
||||
6100 21481.553 104.57796 0 3684.8368 -16.524974
|
||||
6150 20354.4 292.57675 0 3684.9767 2.7960207
|
||||
6200 21326.591 130.75243 0 3685.1843 -1.5929194
|
||||
6250 21505.087 101.07817 0 3685.2593 -3.7821931
|
||||
6300 21296.273 135.6593 0 3685.0382 -0.55635908
|
||||
6350 21295.389 135.86485 0 3685.0964 5.6614093
|
||||
6400 16552.242 926.02655 0 3684.7336 14.177218
|
||||
6450 20148.951 327.1151 0 3685.2736 7.4561085
|
||||
6500 20962.151 191.79415 0 3685.486 -4.5436711
|
||||
6550 21710.328 67.433972 0 3685.8219 -5.7678572
|
||||
6600 20698.571 234.79099 0 3684.5528 -2.1984068
|
||||
6650 17892.287 704.05484 0 3686.1026 11.525836
|
||||
6700 21272.999 141.26589 0 3686.7657 0.44088069
|
||||
6750 19558.993 426.46448 0 3686.2966 -16.907401
|
||||
6800 20350.247 295.23951 0 3686.9474 1.1284348
|
||||
6850 18665.05 573.5326 0 3684.3742 17.088712
|
||||
6900 19769.199 392.1551 0 3687.0216 6.7562425
|
||||
6950 19439.159 446.99138 0 3686.8512 -6.0105763
|
||||
7000 19379.907 456.53471 0 3686.5192 -9.0505095
|
||||
7050 19983.754 356.02523 0 3686.651 -5.6274314
|
||||
7100 19867.737 375.47627 0 3686.7658 17.315482
|
||||
7150 19258.794 477.47344 0 3687.2724 14.316676
|
||||
7200 21282.428 139.96051 0 3687.0318 -0.77043459
|
||||
7250 19828.603 381.98919 0 3686.7564 6.5142869
|
||||
7300 20574.582 257.8245 0 3686.9215 -3.6547118
|
||||
7350 21613.467 84.771568 0 3687.0161 -7.5188826
|
||||
7400 21817.009 50.844944 0 3687.0131 -14.888864
|
||||
7450 14937.538 1197.4257 0 3687.0154 1.7540499
|
||||
7500 18326.914 632.40374 0 3686.8894 8.3397357
|
||||
7550 13611.007 1418.4727 0 3686.9739 -19.379482
|
||||
7600 19173.985 491.9482 0 3687.6123 17.229001
|
||||
7650 16911.504 867.33649 0 3685.9204 -21.042834
|
||||
7700 21752.116 61.143705 0 3686.4963 -10.344487
|
||||
7750 20208.337 318.26355 0 3686.3197 13.385814
|
||||
7800 21649.909 77.950987 0 3686.2692 -1.7911084
|
||||
7850 20139.64 329.50319 0 3686.1098 -5.5805093
|
||||
7900 21355.026 126.7642 0 3685.9352 -7.7062172
|
||||
7950 21336.178 129.88925 0 3685.9188 -2.059298
|
||||
8000 21047.596 177.71546 0 3685.6482 0.37963466
|
||||
8050 19217.351 482.62331 0 3685.5152 6.5582595
|
||||
8100 20499.057 268.7173 0 3685.2268 -1.1959737
|
||||
8150 21494.301 102.83829 0 3685.2219 -1.6427647
|
||||
8200 20074.928 339.19817 0 3685.0195 6.285123
|
||||
8250 17335.157 793.47566 0 3682.6685 22.877381
|
||||
8300 17340.544 794.62619 0 3684.7168 3.9147755
|
||||
8350 20529.345 262.51162 0 3684.0691 4.031768
|
||||
8400 18884.747 537.47827 0 3684.9361 22.853404
|
||||
8450 20341.86 293.10484 0 3683.4148 0.33856656
|
||||
8500 19300.282 467.58127 0 3684.2949 12.35507
|
||||
8550 21631.936 78.254534 0 3683.5772 -10.992959
|
||||
8600 20204.913 316.83233 0 3684.3178 20.74228
|
||||
8650 21018.189 181.32054 0 3684.352 1.8412068
|
||||
8700 20161.304 323.97907 0 3684.1964 -2.646629
|
||||
8750 19081.79 504.00155 0 3684.2998 -10.088053
|
||||
8800 20834.489 211.76247 0 3684.1773 14.896336
|
||||
8850 20929.355 196.18335 0 3684.4092 -1.2602398
|
||||
8900 21491.074 102.47788 0 3684.3235 -1.4696758
|
||||
8950 20474.735 271.69461 0 3684.1504 -6.9489258
|
||||
9000 21128.641 162.40732 0 3683.8474 -7.7928168
|
||||
9050 18421.801 614.46442 0 3684.7646 24.40313
|
||||
9100 19301.292 466.98873 0 3683.8707 4.4687046
|
||||
9150 21575.705 88.213763 0 3684.1646 -0.94696984
|
||||
9200 20004.776 350.05448 0 3684.1838 -7.3466605
|
||||
9250 21384.079 120.14472 0 3684.1578 -8.3773844
|
||||
9300 21980.599 20.702393 0 3684.1356 -12.666293
|
||||
9350 21686.606 69.517984 0 3683.9524 -8.8366533
|
||||
9400 20732.704 228.46247 0 3683.9131 -6.4080307
|
||||
9450 19798.859 384.34696 0 3684.1568 7.6198484
|
||||
9500 20270.695 305.22664 0 3683.6758 1.5862486
|
||||
9550 16496.156 935.28481 0 3684.6441 15.001468
|
||||
9600 20642.429 241.08853 0 3681.4934 -9.2159382
|
||||
9650 21292.587 135.4474 0 3684.2119 -0.54770976
|
||||
9700 18888.158 536.60518 0 3684.6315 5.3236926
|
||||
9750 18750.018 559.35922 0 3684.3623 -9.9424949
|
||||
9800 20544.772 259.71076 0 3683.8394 8.732202
|
||||
9850 16698.125 901.90076 0 3684.9216 9.9553329
|
||||
9900 21450.963 109.58687 0 3684.7474 -4.8001999
|
||||
9950 20664.461 240.66995 0 3684.7468 -3.4840781
|
||||
10000 18951.367 526.45428 0 3685.0155 21.512727
|
||||
Loop time of 8.99246 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 9608.051 tau/day, 1112.043 timesteps/s
|
||||
93.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.01308 | 0.038162 | 0.084123 | 14.4 | 0.42
|
||||
Neigh | 0.017227 | 0.032774 | 0.061983 | 10.0 | 0.36
|
||||
Comm | 1.329 | 1.5822 | 1.8017 | 13.5 | 17.60
|
||||
Output | 0.014984 | 0.029676 | 0.046035 | 6.6 | 0.33
|
||||
Modify | 6.8022 | 7.1104 | 7.4356 | 8.6 | 79.07
|
||||
Other | | 0.1992 | | | 2.22
|
||||
|
||||
Nlocal: 20.25 ave 81 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 46.25 ave 95 max 14 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 249.25 ave 997 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 997
|
||||
Ave neighs/atom = 12.3086
|
||||
Neighbor list builds = 993
|
||||
Dangerous builds = 943
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:09
|
||||
@ -1,342 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
1 clusters, 4 bodies, 3 joints, 36 atoms
|
||||
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 5 bodies, 4 joints, 45 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems2
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363)
|
||||
WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363)
|
||||
WARNING: One or more atoms are time integrated more than once (src/modify.cpp:283)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.854 | 3.854 | 3.854 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -2.7403788
|
||||
50 12167.633 1505.5478 0 3758.8133 35.125973
|
||||
100 17556.978 512.66277 0 3763.9549 11.137534
|
||||
150 19579.586 138.04942 0 3763.8987 -29.953971
|
||||
200 19757.51 105.30542 0 3764.1036 -0.030645317
|
||||
250 18218.374 390.10747 0 3763.8804 13.711001
|
||||
300 19383.039 174.40688 0 3763.8586 5.7240693
|
||||
350 20125.986 36.972611 0 3764.0071 1.9559205
|
||||
400 18888.816 266.10975 0 3764.0386 9.6362168
|
||||
450 19307.656 188.2511 0 3763.743 1.9326206
|
||||
500 16331.197 738.56392 0 3762.8597 9.1715579
|
||||
550 19318.722 186.16172 0 3763.7027 3.0115336
|
||||
600 19455.268 161.20621 0 3764.0336 0.55208034
|
||||
650 18487.011 340.03216 0 3763.5528 -8.0359122
|
||||
700 17321.201 556.32471 0 3763.9545 -13.631751
|
||||
750 18979.187 249.04389 0 3763.7082 -2.6072455
|
||||
800 19342.456 181.85552 0 3763.7918 8.1918726
|
||||
850 19070.641 232.19342 0 3763.7936 7.3148472
|
||||
900 19478.873 156.65987 0 3763.8586 2.4284987
|
||||
950 19912.415 76.437437 0 3763.9216 -1.4667227
|
||||
1000 16003.749 802.39753 0 3766.0548 46.642188
|
||||
1050 19859.583 86.64176 0 3764.3424 -2.1961943
|
||||
1100 19229.575 203.61488 0 3764.6473 -10.632365
|
||||
1150 18821.6 279.15861 0 3764.64 -0.89495035
|
||||
1200 19392.695 173.59744 0 3764.8373 1.8508753
|
||||
1250 16459.624 717.32104 0 3765.3995 33.478127
|
||||
1300 19343.863 182.59043 0 3764.7874 0.75890736
|
||||
1350 20019.643 57.503573 0 3764.8448 0.31444671
|
||||
1400 18549.582 329.31436 0 3764.4221 10.738303
|
||||
1450 15163.926 957.47585 0 3765.6103 -17.923459
|
||||
1500 19223.688 204.15175 0 3764.0939 -1.6134531
|
||||
1550 18147.996 404.12677 0 3764.8668 8.4194779
|
||||
1600 18615.043 317.42467 0 3764.6548 -2.3288934
|
||||
1650 20120.654 38.887913 0 3764.935 -8.7620277
|
||||
1700 19450.907 162.98272 0 3765.0025 2.3254731
|
||||
1750 19374.632 177.37966 0 3765.2744 8.9328774
|
||||
1800 19424.404 167.93966 0 3765.0514 0.081230261
|
||||
1850 17936.249 442.84231 0 3764.3699 6.6010636
|
||||
1900 19982.595 64.406198 0 3764.8868 -2.9529813
|
||||
1950 16215.852 761.91287 0 3764.8485 13.994708
|
||||
2000 18584.422 322.12049 0 3763.68 7.1654003
|
||||
2050 20107.965 41.025754 0 3764.723 -0.3109069
|
||||
2100 20002.333 60.593017 0 3764.7288 -6.7919784
|
||||
2150 16949.762 626.59623 0 3765.441 3.508941
|
||||
2200 20010.953 58.808279 0 3764.5403 -10.862172
|
||||
2250 18982.73 247.00892 0 3762.3292 -0.53807815
|
||||
2300 18401.298 354.87973 0 3762.5274 1.0920554
|
||||
2350 19390.524 172.9415 0 3763.7793 -3.3524932
|
||||
2400 16080.801 786.38838 0 3764.3146 -16.200514
|
||||
2450 18870.412 268.74976 0 3763.2705 11.197736
|
||||
2500 19688.29 117.58223 0 3763.5618 4.382644
|
||||
2550 18870.825 268.78678 0 3763.384 -5.6623656
|
||||
2600 17019.35 611.70808 0 3763.4395 6.3109641
|
||||
2650 18753.285 291.0596 0 3763.8902 2.4120296
|
||||
2700 19742.456 107.20901 0 3763.2193 -0.33061303
|
||||
2750 19522.438 148.16759 0 3763.4339 -1.6254851
|
||||
2800 18304.801 372.55152 0 3762.3295 22.6368
|
||||
2850 18465.36 343.48495 0 3762.9961 4.4169272
|
||||
2900 20151.999 31.372926 0 3763.2245 1.2013699
|
||||
2950 15498.143 892.80071 0 3762.8272 13.263724
|
||||
3000 18728.301 294.65113 0 3762.855 8.1897838
|
||||
3050 18538.466 330.25223 0 3763.3015 8.5865739
|
||||
3100 19081.409 229.5907 0 3763.1849 -4.8573813
|
||||
3150 18498.802 337.11548 0 3762.8195 1.0555321
|
||||
3200 19925.897 73.358029 0 3763.339 -7.7325108
|
||||
3250 19780.108 100.23785 0 3763.2209 -5.5974972
|
||||
3300 19221.043 203.82387 0 3763.2763 4.2703251
|
||||
3350 19025.292 240.11329 0 3763.3156 5.7708328
|
||||
3400 18153.696 401.52086 0 3763.3164 21.076943
|
||||
3450 18611.375 316.50396 0 3763.0548 -3.5484945
|
||||
3500 19931.319 71.969274 0 3762.9543 1.8764978
|
||||
3550 19747.562 106.05439 0 3763.0103 -2.5506186
|
||||
3600 18491.39 338.4134 0 3762.7449 -4.0527808
|
||||
3650 19757.998 104.19207 0 3763.0806 1.4865598
|
||||
3700 20108.003 39.345514 0 3763.0498 0.062827129
|
||||
3750 19222.505 203.28065 0 3763.0039 0.33719277
|
||||
3800 19286.383 191.08831 0 3762.6406 -0.1826802
|
||||
3850 19450.083 161.09138 0 3762.9587 -0.2708263
|
||||
3900 18002.304 429.25655 0 3763.0166 -4.6832439
|
||||
3950 17186.829 582.26502 0 3765.0111 55.816834
|
||||
4000 16826.434 645.84974 0 3761.856 19.675962
|
||||
4050 19227.526 202.18151 0 3762.8344 -0.2596098
|
||||
4100 19908.792 76.084531 0 3762.8978 -2.796813
|
||||
4150 17821.329 462.63065 0 3762.8768 13.069155
|
||||
4200 19917.133 74.574998 0 3762.9329 -6.4181155
|
||||
4250 19012.618 241.96787 0 3762.823 4.0847974
|
||||
4300 19077.34 229.98133 0 3762.8221 4.324323
|
||||
4350 19361.128 177.47406 0 3762.8681 -7.377974
|
||||
4400 18565.044 324.95107 0 3762.9223 2.5229032
|
||||
4450 19352.406 178.98756 0 3762.7665 0.10862717
|
||||
4500 18482.218 340.15496 0 3762.788 12.518301
|
||||
4550 18359.732 362.83749 0 3762.7879 3.7500902
|
||||
4600 19623.618 128.71624 0 3762.7196 -1.1328521
|
||||
4650 17565.707 509.99904 0 3762.9078 1.7135935
|
||||
4700 19876.052 81.892814 0 3762.6431 0.32476108
|
||||
4750 19022.676 239.92262 0 3762.6403 -0.24613022
|
||||
4800 18862.685 269.24248 0 3762.3324 6.2733979
|
||||
4850 19899.174 77.426145 0 3762.4584 0.42535238
|
||||
4900 18250.865 382.72867 0 3762.5185 23.308462
|
||||
4950 18895.847 263.22651 0 3762.4575 8.0634675
|
||||
5000 19096.705 225.69358 0 3762.1204 3.6816481
|
||||
5050 16546.294 698.91312 0 3763.0416 17.453618
|
||||
5100 19501.208 151.20999 0 3762.5449 -1.1231291
|
||||
5150 19479.879 155.00669 0 3762.3917 -3.983378
|
||||
5200 17397.818 541.23039 0 3763.0485 6.1109992
|
||||
5250 18564.869 324.10557 0 3762.0442 9.2244762
|
||||
5300 16271.663 747.52374 0 3760.7947 -6.5256602
|
||||
5350 19831.418 89.851887 0 3762.3367 -2.3453958
|
||||
5400 18723.697 294.67435 0 3762.0256 4.6822081
|
||||
5450 19547.28 142.21934 0 3762.086 -5.5243408
|
||||
5500 19415.447 166.68729 0 3762.1404 -9.5658991
|
||||
5550 18492.721 337.54773 0 3762.1256 6.5184903
|
||||
5600 19391.389 171.14375 0 3762.1416 -0.53835361
|
||||
5650 18503.465 334.62751 0 3761.1951 4.6580363
|
||||
5700 18153.344 399.91064 0 3761.6409 12.851587
|
||||
5750 18342.297 365.14769 0 3761.8694 2.7148176
|
||||
5800 19583.241 135.64969 0 3762.1758 -1.089608
|
||||
5850 15967.283 804.18382 0 3761.088 11.278762
|
||||
5900 19040.271 235.35509 0 3761.3312 5.1352158
|
||||
5950 17920.962 443.17951 0 3761.8762 4.9621366
|
||||
6000 19100.92 224.3946 0 3761.602 -9.537589
|
||||
6050 17982.119 432.3251 0 3762.3472 -2.851617
|
||||
6100 16233.096 755.46191 0 3761.5908 25.113316
|
||||
6150 18316.543 370.01118 0 3761.9635 -1.7445703
|
||||
6200 18483.464 339.13282 0 3761.9966 -2.0857447
|
||||
6250 18609.406 315.56032 0 3761.7467 -12.289208
|
||||
6300 17167.919 582.68212 0 3761.9264 -3.8263397
|
||||
6350 17870.329 452.58116 0 3761.9013 -3.3843134
|
||||
6400 19309.717 186.11786 0 3761.9913 -4.9462739
|
||||
6450 17964.073 435.39924 0 3762.0794 12.272972
|
||||
6500 18772.847 285.61959 0 3762.0727 6.7928648
|
||||
6550 18915.116 259.41365 0 3762.213 -4.1449761
|
||||
6600 19446.628 161.18763 0 3762.415 -2.1906581
|
||||
6650 16348.787 734.99282 0 3762.546 -9.9624546
|
||||
6700 19066.684 231.43863 0 3762.3061 -5.362833
|
||||
6750 14890.323 1004.547 0 3762.0143 37.373013
|
||||
6800 18235.19 385.253 0 3762.1401 0.21012662
|
||||
6850 16447.997 716.11276 0 3762.0382 -9.2095411
|
||||
6900 18343.362 364.81902 0 3761.7379 10.417932
|
||||
6950 16014.084 797.13348 0 3762.7046 6.7906777
|
||||
7000 19120.393 221.29236 0 3762.1059 -1.3461375
|
||||
7050 18055.409 418.30136 0 3761.8957 1.5772317
|
||||
7100 18407.231 353.41868 0 3762.1652 0.61071769
|
||||
7150 18728.136 293.64021 0 3761.8136 5.1649654
|
||||
7200 17706.628 483.07628 0 3762.0815 18.000708
|
||||
7250 19349.505 178.89673 0 3762.1385 2.540201
|
||||
7300 20016.293 55.389159 0 3762.1101 -1.5793163
|
||||
7350 19398.573 169.86661 0 3762.1949 -5.060123
|
||||
7400 19466.526 157.37407 0 3762.2862 1.7158273
|
||||
7450 18440.348 347.09196 0 3761.9712 12.781963
|
||||
7500 19989.907 60.555934 0 3762.3906 -1.5033319
|
||||
7550 19667.28 120.27403 0 3762.363 -3.3502366
|
||||
7600 18497.707 336.15863 0 3761.66 1.7887539
|
||||
7650 17901.957 447.17282 0 3762.3501 0.016725252
|
||||
7700 19758.725 103.3129 0 3762.3361 -23.534448
|
||||
7750 19443.957 161.6532 0 3762.386 -10.323924
|
||||
7800 19776.178 100.1773 0 3762.4324 6.0854422
|
||||
7850 19242.512 198.86705 0 3762.2952 5.2823659
|
||||
7900 19499.929 151.30366 0 3762.4017 12.299911
|
||||
7950 19630.317 127.19541 0 3762.4393 8.0799632
|
||||
8000 19872.384 82.421129 0 3762.4923 2.2126691
|
||||
8050 17747.038 476.27982 0 3762.7683 -7.7042786
|
||||
8100 18832.654 274.78106 0 3762.3095 13.882157
|
||||
8150 19949.814 68.09711 0 3762.5072 -0.54410896
|
||||
8200 17555.866 511.02517 0 3762.1115 6.2471175
|
||||
8250 17800.1 465.9992 0 3762.314 13.583485
|
||||
8300 19755.224 103.89732 0 3762.2721 -1.487243
|
||||
8350 17583.61 506.17539 0 3762.3995 -9.7819128
|
||||
8400 18529.003 330.75623 0 3762.0532 14.731228
|
||||
8450 20155.902 29.797078 0 3762.3716 -8.5711085
|
||||
8500 18047.548 420.54645 0 3762.685 7.3875118
|
||||
8550 19790.794 97.493375 0 3762.4553 -3.3427911
|
||||
8600 19997.902 59.172074 0 3762.4874 3.3479688
|
||||
8650 19987.319 61.148363 0 3762.5037 -1.889232
|
||||
8700 19363.91 176.41833 0 3762.3276 -9.4291288
|
||||
8750 18712.689 296.3979 0 3761.7107 5.9221369
|
||||
8800 19783.17 98.860518 0 3762.4105 -3.5262066
|
||||
8850 18796.049 281.60057 0 3762.3504 -8.2913002
|
||||
8900 16738.277 662.62261 0 3762.3035 8.5838631
|
||||
8950 17869.613 452.25006 0 3761.4377 11.561101
|
||||
9000 18682.512 302.27997 0 3762.0043 3.8878724
|
||||
9050 17513.759 518.50265 0 3761.7914 23.05778
|
||||
9100 17500.686 521.57944 0 3762.4473 -2.8435751
|
||||
9150 19645.683 124.43597 0 3762.5254 -3.0193092
|
||||
9200 18898.897 262.76552 0 3762.5612 3.5891701
|
||||
9250 20114.279 37.614866 0 3762.4813 -0.58120871
|
||||
9300 19562.613 139.54073 0 3762.2468 -3.2630158
|
||||
9350 19679.811 118.05865 0 3762.468 -3.4644363
|
||||
9400 19297.384 188.84527 0 3762.4349 0.40498037
|
||||
9450 18267.029 379.52581 0 3762.309 -0.13762867
|
||||
9500 19951.072 67.63844 0 3762.2814 -7.575539
|
||||
9550 19134.562 218.46835 0 3761.9057 -1.9626244
|
||||
9600 19089.093 227.29178 0 3762.3089 -1.94158
|
||||
9650 16964.603 620.71289 0 3762.3061 16.987042
|
||||
9700 18846.881 271.3129 0 3761.4761 3.4458802
|
||||
9750 19309.225 186.0142 0 3761.7966 9.4048627
|
||||
9800 16359.704 733.51007 0 3763.0849 15.870164
|
||||
9850 19958.532 66.203725 0 3762.2282 6.0043645
|
||||
9900 19864.564 83.502384 0 3762.1253 -0.65360617
|
||||
9950 18996.789 244.25101 0 3762.1749 -2.4961826
|
||||
10000 17933.494 441.33587 0 3762.3532 -6.0731708
|
||||
Loop time of 6.84978 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 12613.550 tau/day, 1459.902 timesteps/s
|
||||
96.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.1054 | 0.1054 | 0.1054 | 0.0 | 1.54
|
||||
Neigh | 0.081336 | 0.081336 | 0.081336 | 0.0 | 1.19
|
||||
Comm | 0.017124 | 0.017124 | 0.017124 | 0.0 | 0.25
|
||||
Output | 0.0050254 | 0.0050254 | 0.0050254 | 0.0 | 0.07
|
||||
Modify | 6.6313 | 6.6313 | 6.6313 | 0.0 | 96.81
|
||||
Other | | 0.00962 | | | 0.14
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 71 ave 71 max 71 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 612 ave 612 max 612 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 612
|
||||
Ave neighs/atom = 7.55556
|
||||
Neighbor list builds = 989
|
||||
Dangerous builds = 906
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:06
|
||||
@ -1,342 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
1 clusters, 4 bodies, 3 joints, 36 atoms
|
||||
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 5 bodies, 4 joints, 45 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
|
||||
#dump 1 all atom 50 dump.rigid.poems2
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363)
|
||||
WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363)
|
||||
WARNING: One or more atoms are time integrated more than once (src/modify.cpp:283)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 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 = 18 18 18
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.919 | 4.201 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -2.7403788
|
||||
50 12167.633 1505.5478 0 3758.8133 35.125973
|
||||
100 17556.978 512.66277 0 3763.9549 11.137534
|
||||
150 19579.586 138.04942 0 3763.8987 -29.953971
|
||||
200 19757.51 105.30542 0 3764.1036 -0.030645317
|
||||
250 18218.374 390.10747 0 3763.8804 13.711001
|
||||
300 19383.039 174.40688 0 3763.8586 5.7240693
|
||||
350 20125.986 36.972611 0 3764.0071 1.9559205
|
||||
400 18888.816 266.10975 0 3764.0386 9.6362168
|
||||
450 19307.656 188.2511 0 3763.743 1.9326206
|
||||
500 16331.197 738.56392 0 3762.8597 9.1715579
|
||||
550 19318.722 186.16172 0 3763.7027 3.0115336
|
||||
600 19455.268 161.20621 0 3764.0336 0.55208034
|
||||
650 18487.011 340.03216 0 3763.5528 -8.0359122
|
||||
700 17321.201 556.32471 0 3763.9545 -13.631751
|
||||
750 18979.187 249.04389 0 3763.7082 -2.6072455
|
||||
800 19342.456 181.85552 0 3763.7918 8.1918726
|
||||
850 19070.641 232.19342 0 3763.7936 7.3148472
|
||||
900 19478.873 156.65987 0 3763.8586 2.4284987
|
||||
950 19912.415 76.437437 0 3763.9216 -1.4667227
|
||||
1000 16003.749 802.39753 0 3766.0548 46.642188
|
||||
1050 19859.583 86.64176 0 3764.3424 -2.1961943
|
||||
1100 19229.575 203.61488 0 3764.6473 -10.632365
|
||||
1150 18821.6 279.15861 0 3764.64 -0.89495035
|
||||
1200 19392.695 173.59744 0 3764.8373 1.8508753
|
||||
1250 16459.624 717.32104 0 3765.3995 33.478127
|
||||
1300 19343.863 182.59043 0 3764.7874 0.75890736
|
||||
1350 20019.643 57.503573 0 3764.8448 0.31444671
|
||||
1400 18549.582 329.31436 0 3764.4221 10.738303
|
||||
1450 15163.926 957.47585 0 3765.6103 -17.923459
|
||||
1500 19223.688 204.15176 0 3764.0939 -1.6134529
|
||||
1550 18147.996 404.12677 0 3764.8668 8.4194781
|
||||
1600 18615.043 317.42468 0 3764.6548 -2.3288926
|
||||
1650 20120.654 38.887908 0 3764.935 -8.7620288
|
||||
1700 19450.907 162.98267 0 3765.0025 2.3254739
|
||||
1750 19374.631 177.3797 0 3765.2744 8.9328773
|
||||
1800 19424.404 167.93965 0 3765.0514 0.081228843
|
||||
1850 17936.227 442.84645 0 3764.3699 6.6011251
|
||||
1900 19982.595 64.406244 0 3764.8868 -2.952971
|
||||
1950 16215.818 761.91942 0 3764.8486 13.994877
|
||||
2000 18584.433 322.11846 0 3763.6801 7.1653695
|
||||
2050 20107.965 41.025796 0 3764.723 -0.31089763
|
||||
2100 20002.329 60.593879 0 3764.7288 -6.7919882
|
||||
2150 16949.817 626.58598 0 3765.4409 3.5087505
|
||||
2200 20010.954 58.8082 0 3764.5403 -10.862143
|
||||
2250 18982.732 247.00854 0 3762.3293 -0.53812607
|
||||
2300 18401.276 354.88369 0 3762.5274 1.0921058
|
||||
2350 19390.535 172.93951 0 3763.7793 -3.3524354
|
||||
2400 16080.475 786.44896 0 3764.3146 -16.201558
|
||||
2450 18870.293 268.77171 0 3763.2704 11.199749
|
||||
2500 19688.508 117.54164 0 3763.5617 4.3806994
|
||||
2550 18870.328 268.87896 0 3763.3841 -5.6641099
|
||||
2600 17020.211 611.54841 0 3763.4394 6.3081434
|
||||
2650 18748.838 291.88478 0 3763.8917 2.4175163
|
||||
2700 19743.991 106.92945 0 3763.224 -0.33916964
|
||||
2750 19525.446 147.60906 0 3763.4324 -1.6251174
|
||||
2800 18257.411 381.40184 0 3762.4038 23.39495
|
||||
2850 18496.796 337.65425 0 3762.9868 4.3657735
|
||||
2900 20163.418 29.253902 0 3763.2203 1.4431917
|
||||
2950 16823.317 646.69817 0 3762.1273 4.9041552
|
||||
3000 19223.007 203.2529 0 3763.069 4.0414458
|
||||
3050 17391.02 542.93746 0 3763.4968 15.139863
|
||||
3100 19205.6 206.57791 0 3763.1705 4.8519241
|
||||
3150 19835.659 90.247763 0 3763.5179 -14.900053
|
||||
3200 18962.776 251.5838 0 3763.2089 -13.706561
|
||||
3250 19418.837 167.29058 0 3763.3716 -2.0866468
|
||||
3300 18628.291 313.69067 0 3763.3742 5.9919715
|
||||
3350 17465.974 529.14439 0 3763.5841 14.122593
|
||||
3400 18488.661 339.6186 0 3763.4448 21.526798
|
||||
3450 19163.152 214.26098 0 3762.9928 4.1888096
|
||||
3500 18000.27 429.81789 0 3763.2011 5.4734485
|
||||
3550 19582.423 136.71887 0 3763.0935 -2.5335675
|
||||
3600 19634.325 127.2219 0 3763.208 -1.9728322
|
||||
3650 19428.114 165.40707 0 3763.2059 -2.3318779
|
||||
3700 19861.116 85.356944 0 3763.3414 -3.9097609
|
||||
3750 19337.239 182.43992 0 3763.4102 -3.3559651
|
||||
3800 19493.146 153.40349 0 3763.2453 -0.71089657
|
||||
3850 18607.616 317.74889 0 3763.6037 3.475832
|
||||
3900 19719.59 111.5553 0 3763.3313 0.58876668
|
||||
3950 19756.661 104.5522 0 3763.1931 3.7526698
|
||||
4000 17904.708 447.1673 0 3762.854 12.270654
|
||||
4050 19588.087 135.80435 0 3763.2279 0.94578945
|
||||
4100 19065.901 232.38235 0 3763.1048 -2.7495195
|
||||
4150 18775.075 286.2257 0 3763.0915 -3.7039858
|
||||
4200 18800.725 281.46601 0 3763.0817 0.15619543
|
||||
4250 19732.687 108.90618 0 3763.1075 3.0865861
|
||||
4300 18278.151 377.63653 0 3762.4794 1.5768601
|
||||
4350 17915.757 445.4804 0 3763.2133 -3.7040484
|
||||
4400 15987.794 802.41575 0 3763.1183 22.252078
|
||||
4450 19302.37 188.69495 0 3763.2079 0.91081327
|
||||
4500 20039.32 52.304099 0 3763.2893 -2.0828905
|
||||
4550 19535.953 145.4374 0 3763.2064 -3.3804255
|
||||
4600 19700.723 114.79823 0 3763.0803 -1.1761163
|
||||
4650 17804.641 465.85788 0 3763.0136 7.5947192
|
||||
4700 19913.881 75.240289 0 3762.996 -2.1100557
|
||||
4750 19982.484 62.535995 0 3762.996 -4.5821237
|
||||
4800 17400.76 540.21707 0 3762.58 -5.8418778
|
||||
4850 19199.88 206.90989 0 3762.4433 3.4536341
|
||||
4900 19173.92 212.11327 0 3762.8392 5.0387071
|
||||
4950 19236.635 200.57537 0 3762.9152 -1.4932783
|
||||
5000 19077.616 230.04967 0 3762.9415 4.3742655
|
||||
5050 19893.763 78.909747 0 3762.94 -1.5796711
|
||||
5100 18884.746 265.68301 0 3762.8583 2.2767949
|
||||
5150 17417.096 537.54036 0 3762.9286 -2.8632555
|
||||
5200 18247.844 383.60092 0 3762.8312 10.384179
|
||||
5250 19494.107 152.60532 0 3762.6251 -4.7617287
|
||||
5300 18739.781 292.46206 0 3762.7919 23.210048
|
||||
5350 19310.938 186.62363 0 3762.7232 14.895327
|
||||
5400 19540.39 144.14287 0 3762.7336 6.094624
|
||||
5450 20074.459 45.247888 0 3762.7403 -2.0871835
|
||||
5500 19986.377 61.668045 0 3762.849 -2.4551918
|
||||
5550 19038.904 237.07578 0 3762.7987 5.4250813
|
||||
5600 19439.124 163.1438 0 3762.9816 4.1291468
|
||||
5650 19480.321 155.58325 0 3763.0501 -3.5308058
|
||||
5700 19869.291 83.651379 0 3763.1497 -7.8661592
|
||||
5750 19991.447 61.068554 0 3763.1884 -6.8473586
|
||||
5800 19454.072 160.36805 0 3762.9739 1.527662
|
||||
5850 17994.409 430.95597 0 3763.2539 -5.6078082
|
||||
5900 19209.794 205.74997 0 3763.1193 8.4113055
|
||||
5950 19046.427 236.06321 0 3763.1793 10.463356
|
||||
6000 19409.899 168.95271 0 3763.3785 2.542067
|
||||
6050 18068.174 417.35443 0 3763.3125 10.498199
|
||||
6100 19549.253 143.21885 0 3763.4509 2.3075797
|
||||
6150 18464.719 344.0303 0 3763.4228 0.46469762
|
||||
6200 19811.205 94.62725 0 3763.3689 1.2382763
|
||||
6250 18715.36 297.26445 0 3763.0718 -3.4541762
|
||||
6300 17115.664 594.09913 0 3763.6666 4.2065564
|
||||
6350 18155.927 400.71764 0 3762.9264 1.1521258
|
||||
6400 19873.093 83.169067 0 3763.3716 0.16383592
|
||||
6450 19991.88 61.13218 0 3763.3321 -1.3008128
|
||||
6500 19434.416 164.40698 0 3763.3728 -13.593422
|
||||
6550 19855.253 86.645329 0 3763.544 -0.85704037
|
||||
6600 19251.141 198.41152 0 3763.4376 4.3027745
|
||||
6650 19741.815 107.69047 0 3763.582 4.994835
|
||||
6700 19633.466 127.69333 0 3763.5203 6.3677145
|
||||
6750 16231.353 757.83705 0 3763.6431 -1.5978692
|
||||
6800 18863.396 270.1114 0 3763.3329 -11.915909
|
||||
6850 19644.779 125.29421 0 3763.2163 -1.151217
|
||||
6900 18883.642 266.06889 0 3763.0397 -4.3950749
|
||||
6950 19042.364 236.54144 0 3762.9052 5.5718878
|
||||
7000 18351.868 364.38028 0 3762.8743 7.8958273
|
||||
7050 19981.031 62.840667 0 3763.0316 -5.8572298
|
||||
7100 19796.372 97.073665 0 3763.0685 -3.5178361
|
||||
7150 19805.385 95.235221 0 3762.899 -2.5481726
|
||||
7200 18722.055 295.86113 0 3762.9084 13.826356
|
||||
7250 19537.304 144.54234 0 3762.5616 1.2288666
|
||||
7300 18787.328 283.49504 0 3762.6299 9.0044469
|
||||
7350 18886.005 265.52121 0 3762.9295 6.6791881
|
||||
7400 19891.864 79.239278 0 3762.9178 -2.3882842
|
||||
7450 18164.752 399.07065 0 3762.9137 3.9400481
|
||||
7500 18702.612 299.582 0 3763.0286 4.7987316
|
||||
7550 19884.986 80.231665 0 3762.6365 -0.75016515
|
||||
7600 19549.059 142.16243 0 3762.3586 -2.1035756
|
||||
7650 18223.668 387.9047 0 3762.658 -17.064339
|
||||
7700 19428.4 164.79531 0 3762.6473 -2.8342541
|
||||
7750 19239.584 199.93029 0 3762.8163 3.1746033
|
||||
7800 19458.005 159.46176 0 3762.7961 1.714515
|
||||
7850 18320.308 369.77051 0 3762.4202 2.1422976
|
||||
7900 18817.415 278.04812 0 3762.7546 0.94492621
|
||||
7950 19892.761 79.115928 0 3762.9606 1.4948501
|
||||
8000 19592.344 134.7639 0 3762.9758 -1.8520224
|
||||
8050 19316.109 185.70579 0 3762.7631 -4.8061205
|
||||
8100 19867.017 83.850395 0 3762.9277 -3.496391
|
||||
8150 19129.936 220.29802 0 3762.8789 -2.8357376
|
||||
8200 18449.554 346.30415 0 3762.8883 1.4417837
|
||||
8250 18405.197 354.49049 0 3762.8602 6.7020283
|
||||
8300 18310.437 372.25376 0 3763.0755 3.9043508
|
||||
8350 18842.702 273.55075 0 3762.94 -10.987272
|
||||
8400 18574.308 323.33378 0 3763.0204 12.008785
|
||||
8450 15368.628 918.21692 0 3764.2591 34.80292
|
||||
8500 18432.887 349.54013 0 3763.0378 0.00064258465
|
||||
8550 15777.73 841.79263 0 3763.5945 15.473699
|
||||
8600 17205.381 576.4515 0 3762.6331 2.3985544
|
||||
8650 19773.742 101.48276 0 3763.2869 2.3978892
|
||||
8700 19059.824 232.99716 0 3762.5941 5.2611349
|
||||
8750 19006.086 243.41125 0 3763.0568 4.7880403
|
||||
8800 19492.691 153.0188 0 3762.7763 1.9118755
|
||||
8850 19625.883 128.44474 0 3762.8675 3.4157389
|
||||
8900 19916.97 74.635094 0 3762.9629 -10.157254
|
||||
8950 16012.956 798.16801 0 3763.5302 16.904998
|
||||
9000 19364.051 177.00354 0 3762.9389 -13.373346
|
||||
9050 19133.929 219.61882 0 3762.9389 -7.3824392
|
||||
9100 18657.168 307.85939 0 3762.8905 9.3071421
|
||||
9150 17975.904 434.21548 0 3763.0867 6.9609506
|
||||
9200 19075.282 230.41699 0 3762.8767 7.0961232
|
||||
9250 20115.276 37.578674 0 3762.6298 1.8678552
|
||||
9300 18195.486 393.20682 0 3762.7413 13.272552
|
||||
9350 19617.155 129.85893 0 3762.6653 -2.0849447
|
||||
9400 19276.325 193.03425 0 3762.724 -2.8963555
|
||||
9450 18642.803 310.4759 0 3762.8467 3.407984
|
||||
9500 19175.951 211.72785 0 3762.8298 -0.39025564
|
||||
9550 17669.191 490.85942 0 3762.9319 5.3867954
|
||||
9600 18481.199 340.29485 0 3762.7391 8.9004886
|
||||
9650 20091.442 42.504743 0 3763.1422 -1.3206133
|
||||
9700 19651.405 124.04835 0 3763.1975 1.4000525
|
||||
9750 19138.245 219.03637 0 3763.1558 5.8352794
|
||||
9800 19189.146 209.67958 0 3763.2251 6.214691
|
||||
9850 19899.376 78.096337 0 3763.166 -0.75102404
|
||||
9900 19447.247 161.27279 0 3762.6149 -6.4166376
|
||||
9950 19807.083 95.152663 0 3763.1309 -0.88933698
|
||||
10000 18972.157 249.56342 0 3762.9258 1.9189241
|
||||
Loop time of 9.05599 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Performance: 9540.646 tau/day, 1104.241 timesteps/s
|
||||
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.009043 | 0.030098 | 0.048276 | 8.1 | 0.33
|
||||
Neigh | 0.012702 | 0.02622 | 0.04009 | 6.1 | 0.29
|
||||
Comm | 0.99902 | 1.2924 | 1.6008 | 24.3 | 14.27
|
||||
Output | 0.0057414 | 0.010684 | 0.024912 | 7.9 | 0.12
|
||||
Modify | 7.2674 | 7.5881 | 7.9123 | 10.6 | 83.79
|
||||
Other | | 0.1085 | | | 1.20
|
||||
|
||||
Nlocal: 20.25 ave 37 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 17.75 ave 33 max 4 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 144.75 ave 356 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 579
|
||||
Ave neighs/atom = 7.14815
|
||||
Neighbor list builds = 994
|
||||
Dangerous builds = 958
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:09
|
||||
14
examples/rigid/unconnected-bodies.dat
Normal file
14
examples/rigid/unconnected-bodies.dat
Normal file
@ -0,0 +1,14 @@
|
||||
# Body definition file for POEMS fix
|
||||
# 9 individual rigid bodies
|
||||
|
||||
# Format
|
||||
# Body-ID Body-Type Atom-ID1 Atom-ID2 ...
|
||||
1 1 1 2 3 4 5 6 7 8 9
|
||||
2 2 10 11 12 13 14 15 16 17 18
|
||||
3 1 19 20 21 22 23 24 25 26 27
|
||||
4 2 28 29 30 31 32 33 34 35 36
|
||||
5 3 37 38 39 40 41 42 43 44 45
|
||||
6 1 46 47 48 49 50 51 52 53 54
|
||||
7 2 55 56 57 58 59 60 61 62 63
|
||||
8 1 64 65 66 67 68 69 70 71 72
|
||||
9 2 73 74 75 76 77 78 79 80 81
|
||||
@ -1,4 +1,3 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -20,22 +19,24 @@
|
||||
|
||||
#include "fix_poems.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
#include "workspace.h"
|
||||
#include "atom.h"
|
||||
#include "citeme.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#include "respa.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "group.h"
|
||||
#include "comm.h"
|
||||
#include "citeme.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "math_eigen.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "respa.h"
|
||||
#include "text_file_reader.h"
|
||||
#include "update.h"
|
||||
#include "workspace.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include <vector>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
@ -61,12 +62,11 @@ static const char cite_fix_poems[] =
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg), step_respa(nullptr), natom2body(nullptr),
|
||||
atom2body(nullptr), displace(nullptr), nrigid(nullptr), masstotal(nullptr),
|
||||
xcm(nullptr), vcm(nullptr), fcm(nullptr), inertia(nullptr), ex_space(nullptr),
|
||||
ey_space(nullptr), ez_space(nullptr), angmom(nullptr), omega(nullptr),
|
||||
torque(nullptr), sum(nullptr), all(nullptr), jointbody(nullptr),
|
||||
xjoint(nullptr), freelist(nullptr), poems(nullptr)
|
||||
Fix(lmp, narg, arg), step_respa(nullptr), natom2body(nullptr), atom2body(nullptr),
|
||||
displace(nullptr), nrigid(nullptr), masstotal(nullptr), xcm(nullptr), vcm(nullptr),
|
||||
fcm(nullptr), inertia(nullptr), ex_space(nullptr), ey_space(nullptr), ez_space(nullptr),
|
||||
angmom(nullptr), omega(nullptr), torque(nullptr), sum(nullptr), all(nullptr),
|
||||
jointbody(nullptr), xjoint(nullptr), freelist(nullptr), poems(nullptr)
|
||||
{
|
||||
if (lmp->citeme) lmp->citeme->add(cite_fix_poems);
|
||||
|
||||
@ -79,8 +79,6 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
thermo_virial = 1;
|
||||
dof_flag = 1;
|
||||
|
||||
MPI_Comm_rank(world,&me);
|
||||
|
||||
// perform initial allocation of atom-based arrays
|
||||
// register with atom class
|
||||
|
||||
@ -120,8 +118,7 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
int *igroups = new int[nbody];
|
||||
for (ibody = 0; ibody < nbody; ibody++) {
|
||||
igroups[ibody] = group->find(arg[ibody + 4]);
|
||||
if (igroups[ibody] == -1)
|
||||
error->all(FLERR,"Could not find fix poems group ID");
|
||||
if (igroups[ibody] == -1) error->all(FLERR, "Could not find fix poems group ID");
|
||||
}
|
||||
|
||||
int *mask = atom->mask;
|
||||
@ -158,8 +155,7 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
} else if (strcmp(arg[3], "molecule") == 0) {
|
||||
if (narg != 4) error->all(FLERR, "Illegal fix poems command");
|
||||
if (atom->molecular == Atom::ATOMIC)
|
||||
error->all(FLERR,
|
||||
"Must use a molecular atom style with fix poems molecule");
|
||||
error->all(FLERR, "Must use a molecular atom style with fix poems molecule");
|
||||
|
||||
int *mask = atom->mask;
|
||||
tagint *molecule = atom->molecule;
|
||||
@ -171,8 +167,7 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
tagint itmp;
|
||||
MPI_Allreduce(&maxmol_tag, &itmp, 1, MPI_LMP_TAGINT, MPI_MAX, world);
|
||||
if (itmp+1 > MAXSMALLINT)
|
||||
error->all(FLERR,"Too many molecules for fix poems");
|
||||
if (itmp + 1 > MAXSMALLINT) error->all(FLERR, "Too many molecules for fix poems");
|
||||
int maxmol = (int) itmp;
|
||||
|
||||
int *ncount;
|
||||
@ -188,8 +183,10 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
nbody = 0;
|
||||
for (i = 0; i <= maxmol; i++)
|
||||
if (nall[i]) nall[i] = nbody++;
|
||||
else nall[i] = -1;
|
||||
if (nall[i])
|
||||
nall[i] = nbody++;
|
||||
else
|
||||
nall[i] = -1;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
natom2body[i] = 0;
|
||||
@ -202,7 +199,8 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
memory->destroy(ncount);
|
||||
memory->destroy(nall);
|
||||
|
||||
} else error->all(FLERR,"Illegal fix poems command");
|
||||
} else
|
||||
error->all(FLERR, "Illegal fix poems command");
|
||||
|
||||
// error if no bodies
|
||||
// error if any atom in too many bodies
|
||||
@ -214,8 +212,7 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (natom2body[i] > MAXBODY) flag = 1;
|
||||
int flagall;
|
||||
MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world);
|
||||
if (flagall)
|
||||
error->all(FLERR,"Atom in too many rigid bodies - boost MAXBODY");
|
||||
if (flagall) error->all(FLERR, "Atom in too many rigid bodies - boost MAXBODY");
|
||||
|
||||
// create all nbody-length arrays
|
||||
|
||||
@ -243,8 +240,7 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
for (ibody = 0; ibody < nbody; ibody++) ncount[ibody] = 0;
|
||||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
for (j = 0; j < natom2body[i]; j++)
|
||||
ncount[atom2body[i][j]]++;
|
||||
for (j = 0; j < natom2body[i]; j++) ncount[atom2body[i][j]]++;
|
||||
|
||||
MPI_Allreduce(ncount, nrigid, nbody, MPI_INT, MPI_SUM, world);
|
||||
delete[] ncount;
|
||||
@ -277,9 +273,9 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
for (ibody = 0; ibody < nbody; ibody++) nsum += nrigid[ibody];
|
||||
nsum -= njoint;
|
||||
|
||||
if (me == 0)
|
||||
utils::logmesg(lmp,"{} clusters, {} bodies, {} joints, {} atoms\n",
|
||||
ncluster,nbody,njoint,nsum);
|
||||
if (comm->me == 0)
|
||||
utils::logmesg(lmp, "{} clusters, {} bodies, {} joints, {} atoms\n", ncluster, nbody, njoint,
|
||||
nsum);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -352,34 +348,24 @@ void FixPOEMS::init()
|
||||
// warn if more than one POEMS fix
|
||||
// if earlyflag, warn if any post-force fixes come after POEMS fix
|
||||
|
||||
int count = 0;
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (strcmp(modify->fix[i]->style,"poems") == 0) count++;
|
||||
if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix poems");
|
||||
if (modify->get_fix_by_style("poems").size() > 1)
|
||||
if (comm->me == 0) error->warning(FLERR, "More than one fix poems");
|
||||
|
||||
if (earlyflag) {
|
||||
int pflag = 0;
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
if (strcmp(modify->fix[i]->style,"poems") == 0) pflag = 1;
|
||||
if (pflag && (modify->fmask[i] & POST_FORCE) &&
|
||||
!modify->fix[i]->rigid_flag) {
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,std::string("Fix ") + modify->fix[i]->id
|
||||
+ std::string(" alters forces after fix poems"));
|
||||
}
|
||||
bool pflag = false;
|
||||
for (auto ifix : modify->get_fix_list()) {
|
||||
if (utils::strmatch(ifix->style, "^poems")) pflag = true;
|
||||
if (pflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
|
||||
if (comm->me == 0) error->warning(FLERR, "Fix {} alters forces after fix poems", ifix->id);
|
||||
}
|
||||
}
|
||||
|
||||
// error if npt,nph fix comes before rigid fix
|
||||
|
||||
for (i = 0; i < modify->nfix; i++) {
|
||||
if (strcmp(modify->fix[i]->style,"npt") == 0) break;
|
||||
if (strcmp(modify->fix[i]->style,"nph") == 0) break;
|
||||
}
|
||||
if (i < modify->nfix) {
|
||||
for (int j = i; j < modify->nfix; j++)
|
||||
if (strcmp(modify->fix[j]->style,"poems") == 0)
|
||||
bool pflag = false;
|
||||
for (auto ifix : modify->get_fix_list()) {
|
||||
if (!pflag && utils::strmatch(ifix->style, "np[th]"))
|
||||
error->all(FLERR, "POEMS fix must come before NPT/NPH fix");
|
||||
if (utils::strmatch(ifix->style, "^poems")) pflag = true;
|
||||
}
|
||||
|
||||
// timestep info
|
||||
@ -426,8 +412,7 @@ void FixPOEMS::init()
|
||||
sum[ibody][1] += (x[i][1] + ybox * yprd) * massone;
|
||||
sum[ibody][2] += (x[i][2] + zbox * zprd) * massone;
|
||||
sum[ibody][3] += massone;
|
||||
sum[ibody][4] += massone *
|
||||
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
|
||||
sum[ibody][4] += massone * (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]);
|
||||
}
|
||||
}
|
||||
|
||||
@ -514,23 +499,18 @@ void FixPOEMS::init()
|
||||
max = MAX(inertia[ibody][0], inertia[ibody][1]);
|
||||
max = MAX(max, inertia[ibody][2]);
|
||||
|
||||
if (inertia[ibody][0] < EPSILON*max ||
|
||||
inertia[ibody][1] < EPSILON*max ||
|
||||
if (inertia[ibody][0] < EPSILON * max || inertia[ibody][1] < EPSILON * max ||
|
||||
inertia[ibody][2] < EPSILON * max)
|
||||
error->all(FLERR, "Rigid body has degenerate moment of inertia");
|
||||
|
||||
// enforce 3 evectors as a right-handed coordinate system
|
||||
// flip 3rd evector if needed
|
||||
|
||||
ez0 = ex_space[ibody][1]*ey_space[ibody][2] -
|
||||
ex_space[ibody][2]*ey_space[ibody][1];
|
||||
ez1 = ex_space[ibody][2]*ey_space[ibody][0] -
|
||||
ex_space[ibody][0]*ey_space[ibody][2];
|
||||
ez2 = ex_space[ibody][0]*ey_space[ibody][1] -
|
||||
ex_space[ibody][1]*ey_space[ibody][0];
|
||||
ez0 = ex_space[ibody][1] * ey_space[ibody][2] - ex_space[ibody][2] * ey_space[ibody][1];
|
||||
ez1 = ex_space[ibody][2] * ey_space[ibody][0] - ex_space[ibody][0] * ey_space[ibody][2];
|
||||
ez2 = ex_space[ibody][0] * ey_space[ibody][1] - ex_space[ibody][1] * ey_space[ibody][0];
|
||||
|
||||
if (ez0*ez_space[ibody][0] + ez1*ez_space[ibody][1] +
|
||||
ez2*ez_space[ibody][2] < 0.0) {
|
||||
if (ez0 * ez_space[ibody][0] + ez1 * ez_space[ibody][1] + ez2 * ez_space[ibody][2] < 0.0) {
|
||||
ez_space[ibody][0] = -ez_space[ibody][0];
|
||||
ez_space[ibody][1] = -ez_space[ibody][1];
|
||||
ez_space[ibody][2] = -ez_space[ibody][2];
|
||||
@ -557,13 +537,11 @@ void FixPOEMS::init()
|
||||
dy = x[i][1] + ybox * yprd - xcm[ibody][1];
|
||||
dz = x[i][2] + zbox * zprd - xcm[ibody][2];
|
||||
|
||||
displace[i][0] = dx*ex_space[ibody][0] + dy*ex_space[ibody][1] +
|
||||
dz*ex_space[ibody][2];
|
||||
displace[i][1] = dx*ey_space[ibody][0] + dy*ey_space[ibody][1] +
|
||||
dz*ey_space[ibody][2];
|
||||
displace[i][2] = dx*ez_space[ibody][0] + dy*ez_space[ibody][1] +
|
||||
dz*ez_space[ibody][2];
|
||||
} else displace[i][0] = displace[i][1] = displace[i][2] = 0.0;
|
||||
displace[i][0] = dx * ex_space[ibody][0] + dy * ex_space[ibody][1] + dz * ex_space[ibody][2];
|
||||
displace[i][1] = dx * ey_space[ibody][0] + dy * ey_space[ibody][1] + dz * ey_space[ibody][2];
|
||||
displace[i][2] = dx * ez_space[ibody][0] + dy * ez_space[ibody][1] + dz * ez_space[ibody][2];
|
||||
} else
|
||||
displace[i][0] = displace[i][1] = displace[i][2] = 0.0;
|
||||
}
|
||||
|
||||
// test for valid principal moments & axes
|
||||
@ -591,12 +569,9 @@ void FixPOEMS::init()
|
||||
dz = x[i][2] + zbox * zprd - xcm[ibody][2];
|
||||
massone = mass[type[i]];
|
||||
|
||||
ddx = dx*ex_space[ibody][0] + dy*ex_space[ibody][1] +
|
||||
dz*ex_space[ibody][2];
|
||||
ddy = dx*ey_space[ibody][0] + dy*ey_space[ibody][1] +
|
||||
dz*ey_space[ibody][2];
|
||||
ddz = dx*ez_space[ibody][0] + dy*ez_space[ibody][1] +
|
||||
dz*ez_space[ibody][2];
|
||||
ddx = dx * ex_space[ibody][0] + dy * ex_space[ibody][1] + dz * ex_space[ibody][2];
|
||||
ddy = dx * ey_space[ibody][0] + dy * ey_space[ibody][1] + dz * ey_space[ibody][2];
|
||||
ddz = dx * ez_space[ibody][0] + dy * ez_space[ibody][1] + dz * ez_space[ibody][2];
|
||||
|
||||
sum[ibody][0] += massone * (ddy * ddy + ddz * ddz);
|
||||
sum[ibody][1] += massone * (ddx * ddx + ddz * ddz);
|
||||
@ -614,8 +589,7 @@ void FixPOEMS::init()
|
||||
fabs(all[ibody][1] - inertia[ibody][1]) > TOLERANCE ||
|
||||
fabs(all[ibody][2] - inertia[ibody][2]) > TOLERANCE)
|
||||
error->all(FLERR, "Bad principal moments");
|
||||
if (fabs(all[ibody][3]) > TOLERANCE ||
|
||||
fabs(all[ibody][4]) > TOLERANCE ||
|
||||
if (fabs(all[ibody][3]) > TOLERANCE || fabs(all[ibody][4]) > TOLERANCE ||
|
||||
fabs(all[ibody][5]) > TOLERANCE)
|
||||
error->all(FLERR, "Bad principal moments");
|
||||
}
|
||||
@ -690,8 +664,8 @@ void FixPOEMS::setup(int vflag)
|
||||
// set velocities from angmom & omega
|
||||
|
||||
for (ibody = 0; ibody < nbody; ibody++)
|
||||
omega_from_mq(angmom[ibody],ex_space[ibody],ey_space[ibody],
|
||||
ez_space[ibody],inertia[ibody],omega[ibody]);
|
||||
omega_from_mq(angmom[ibody], ex_space[ibody], ey_space[ibody], ez_space[ibody], inertia[ibody],
|
||||
omega[ibody]);
|
||||
set_v();
|
||||
|
||||
// guestimate virial as 2x the set_v contribution
|
||||
@ -701,8 +675,7 @@ void FixPOEMS::setup(int vflag)
|
||||
for (n = 0; n < 6; n++) virial[n] *= 2.0;
|
||||
if (vflag_atom) {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
for (n = 0; n < 6; n++)
|
||||
vatom[i][n] *= 2.0;
|
||||
for (n = 0; n < 6; n++) vatom[i][n] *= 2.0;
|
||||
}
|
||||
}
|
||||
|
||||
@ -713,10 +686,9 @@ void FixPOEMS::setup(int vflag)
|
||||
|
||||
// setup for POEMS
|
||||
|
||||
poems->MakeSystem(nbody,masstotal,inertia,xcm,vcm,omega,
|
||||
ex_space,ey_space,ez_space,
|
||||
njoint,jointbody,xjoint,nfree,freelist,
|
||||
dthalf,dtv,force->ftm2v,total_ke);
|
||||
poems->MakeSystem(nbody, masstotal, inertia, xcm, vcm, omega, ex_space, ey_space, ez_space,
|
||||
njoint, jointbody, xjoint, nfree, freelist, dthalf, dtv, force->ftm2v,
|
||||
total_ke);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -839,8 +811,10 @@ void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int /* iloop */)
|
||||
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
|
||||
dthalf = 0.5 * step_respa[ilevel];
|
||||
|
||||
if (ilevel == 0) initial_integrate(vflag);
|
||||
else final_integrate();
|
||||
if (ilevel == 0)
|
||||
initial_integrate(vflag);
|
||||
else
|
||||
final_integrate();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -936,72 +910,55 @@ void FixPOEMS::deform(int /* flag */) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixPOEMS::readfile(char *file)
|
||||
void FixPOEMS::readfile(const char *file)
|
||||
{
|
||||
FILE *fp;
|
||||
|
||||
if (me == 0) {
|
||||
fp = fopen(file,"r");
|
||||
if (fp == nullptr)
|
||||
error->one(FLERR,"Cannot open fix poems file {}: {}",
|
||||
file, utils::getsyserror());
|
||||
}
|
||||
|
||||
nbody = 0;
|
||||
char *line = nullptr;
|
||||
int maxline = 0;
|
||||
char *ptr;
|
||||
int nlocal = atom->nlocal;
|
||||
int i,id,nlen;
|
||||
// read and parse file with bodies on rank 0 and then broadcast and process data
|
||||
std::vector<std::vector<bigint>> bodies;
|
||||
int maxbody = 0;
|
||||
|
||||
if (comm->me == 0) {
|
||||
try {
|
||||
TextFileReader reader(file, "POEMS rigid bodies");
|
||||
while (true) {
|
||||
if (me == 0) nlen = readline(fp,&line,&maxline);
|
||||
MPI_Bcast(&nlen,1,MPI_INT,0,world);
|
||||
if (nlen == 0) break;
|
||||
MPI_Bcast(line,nlen,MPI_CHAR,0,world);
|
||||
|
||||
ptr = strtok(line," ,\t\n\0");
|
||||
if (ptr == nullptr || ptr[0] == '#') continue;
|
||||
ptr = strtok(nullptr," ,\t\n\0");
|
||||
|
||||
while ((ptr = strtok(nullptr," ,\t\n\0"))) {
|
||||
id = atoi(ptr);
|
||||
i = atom->map(id);
|
||||
if (i < 0 || i >= nlocal) continue;
|
||||
if (natom2body[i] < MAXBODY) atom2body[i][natom2body[i]] = nbody;
|
||||
natom2body[i]++;
|
||||
std::vector<bigint> onebody;
|
||||
auto values = reader.next_values(0);
|
||||
values.skip(2); // ignore body id and body type
|
||||
while (values.has_next()) onebody.push_back(values.next_bigint());
|
||||
maxbody = MAX(maxbody, (int) onebody.size());
|
||||
bodies.push_back(onebody);
|
||||
}
|
||||
} catch (EOFException &) {
|
||||
// reached end of file
|
||||
printf("reached EOF\n");
|
||||
} catch (std::exception &e) {
|
||||
error->one(FLERR, "Error reading file with POEMS body definitions: {}", e.what());
|
||||
}
|
||||
nbody++;
|
||||
}
|
||||
|
||||
memory->destroy(line);
|
||||
if (me == 0) fclose(fp);
|
||||
nbody = bodies.size();
|
||||
MPI_Bcast(&nbody, 1, MPI_INT, 0, world);
|
||||
MPI_Bcast(&maxbody, 1, MPI_INT, 0, world);
|
||||
bigint *buf = new bigint[maxbody + 1];
|
||||
const int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nbody; ++i) {
|
||||
if (comm->me == 0) {
|
||||
buf[0] = bodies[i].size();
|
||||
memcpy(buf + 1, bodies[i].data(), bodies[i].size() * sizeof(bigint));
|
||||
}
|
||||
MPI_Bcast(buf, maxbody + 1, MPI_LMP_BIGINT, 0, world);
|
||||
|
||||
// convert global atom ids to local atom indices and fill data structures
|
||||
for (int j = 1; j <= buf[0]; ++j) {
|
||||
int k = atom->map(buf[j]);
|
||||
if (k < 0 || k >= nlocal) continue;
|
||||
if (natom2body[k] < MAXBODY) atom2body[k][natom2body[k]] = i;
|
||||
natom2body[k]++;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixPOEMS::readline(FILE *fp, char **pline, int *pmaxline)
|
||||
{
|
||||
int n = 0;
|
||||
char *line = *pline;
|
||||
int maxline = *pmaxline;
|
||||
|
||||
while (true) {
|
||||
if (n+1 >= maxline) {
|
||||
maxline += DELTA;
|
||||
memory->grow(line,maxline,"fix_poems:line");
|
||||
}
|
||||
if (fgets(&line[n],maxline-n,fp) == nullptr) {
|
||||
n = 0;
|
||||
break;
|
||||
}
|
||||
n = strlen(line);
|
||||
if (n < maxline-1 || line[n-1] == '\n') break;
|
||||
}
|
||||
|
||||
*pmaxline = maxline;
|
||||
*pline = line;
|
||||
return n;
|
||||
delete[] buf;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -1062,11 +1019,11 @@ void FixPOEMS::jointbuild()
|
||||
|
||||
if (njoint) {
|
||||
if (mjoint)
|
||||
MPI_Allgatherv(mylist[0],3*mjoint,MPI_LMP_TAGINT,jlist[0],
|
||||
recvcounts,displs,MPI_LMP_TAGINT,world);
|
||||
MPI_Allgatherv(mylist[0], 3 * mjoint, MPI_LMP_TAGINT, jlist[0], recvcounts, displs,
|
||||
MPI_LMP_TAGINT, world);
|
||||
else
|
||||
MPI_Allgatherv(nullptr,3*mjoint,MPI_LMP_TAGINT,jlist[0],
|
||||
recvcounts,displs,MPI_LMP_TAGINT,world);
|
||||
MPI_Allgatherv(nullptr, 3 * mjoint, MPI_LMP_TAGINT, jlist[0], recvcounts, displs,
|
||||
MPI_LMP_TAGINT, world);
|
||||
}
|
||||
|
||||
delete[] recvcounts;
|
||||
@ -1074,9 +1031,8 @@ void FixPOEMS::jointbuild()
|
||||
|
||||
// warning if no joints
|
||||
|
||||
if (njoint == 0 && me == 0)
|
||||
error->warning(FLERR,
|
||||
"No joints between rigid bodies, use fix rigid instead");
|
||||
if (njoint == 0 && comm->me == 0)
|
||||
error->warning(FLERR, "No joints between rigid bodies, use fix rigid instead");
|
||||
|
||||
// sort joint list in ascending order by body indices
|
||||
// check for loops in joint connections between rigid bodies
|
||||
@ -1084,8 +1040,7 @@ void FixPOEMS::jointbuild()
|
||||
|
||||
sortlist(njoint, jlist);
|
||||
|
||||
if (loopcheck(nbody,njoint,jlist))
|
||||
error->all(FLERR,"Cyclic loop in joint connections");
|
||||
if (loopcheck(nbody, njoint, jlist)) error->all(FLERR, "Cyclic loop in joint connections");
|
||||
|
||||
int *bodyflag = new int[nbody];
|
||||
for (i = 0; i < nbody; i++) bodyflag[i] = 0;
|
||||
@ -1094,8 +1049,7 @@ void FixPOEMS::jointbuild()
|
||||
bodyflag[jlist[i][1]]++;
|
||||
}
|
||||
for (i = 0; i < nbody; i++)
|
||||
if (bodyflag[i] > 2)
|
||||
error->all(FLERR,"Tree structure in joint connections");
|
||||
if (bodyflag[i] > 2) error->all(FLERR, "Tree structure in joint connections");
|
||||
delete[] bodyflag;
|
||||
|
||||
// allocate and setup joint arrays
|
||||
@ -1122,11 +1076,11 @@ void FixPOEMS::jointbuild()
|
||||
myjoint[i][0] = x[j][0];
|
||||
myjoint[i][1] = x[j][1];
|
||||
myjoint[i][2] = x[j][2];
|
||||
} else myjoint[i][0] = myjoint[i][1] = myjoint[i][2] = 0.0;
|
||||
} else
|
||||
myjoint[i][0] = myjoint[i][1] = myjoint[i][2] = 0.0;
|
||||
}
|
||||
|
||||
if (njoint)
|
||||
MPI_Allreduce(myjoint[0],xjoint[0],3*njoint,MPI_DOUBLE,MPI_SUM,world);
|
||||
if (njoint) MPI_Allreduce(myjoint[0], xjoint[0], 3 * njoint, MPI_DOUBLE, MPI_SUM, world);
|
||||
|
||||
// compute freelist of nfree single unconnected bodies
|
||||
// POEMS could do this itself
|
||||
@ -1141,8 +1095,10 @@ void FixPOEMS::jointbuild()
|
||||
nfree = 0;
|
||||
for (i = 0; i < nbody; i++)
|
||||
if (mark[i]) nfree++;
|
||||
if (nfree) freelist = new int[nfree];
|
||||
else freelist = nullptr;
|
||||
if (nfree)
|
||||
freelist = new int[nfree];
|
||||
else
|
||||
freelist = nullptr;
|
||||
nfree = 0;
|
||||
for (i = 0; i < nbody; i++)
|
||||
if (mark[i]) freelist[nfree++] = i + 1;
|
||||
@ -1176,8 +1132,8 @@ void FixPOEMS::sortlist(int n, tagint **list)
|
||||
v2 = list[i - 1][2];
|
||||
j = i;
|
||||
flag = 0;
|
||||
if (list[j-inc-1][0] > v0 ||
|
||||
(list[j-inc-1][0] == v0 && list[j-inc-1][1] > v1)) flag = 1;
|
||||
if (list[j - inc - 1][0] > v0 || (list[j - inc - 1][0] == v0 && list[j - inc - 1][1] > v1))
|
||||
flag = 1;
|
||||
while (flag) {
|
||||
list[j - 1][0] = list[j - inc - 1][0];
|
||||
list[j - 1][1] = list[j - inc - 1][1];
|
||||
@ -1185,8 +1141,8 @@ void FixPOEMS::sortlist(int n, tagint **list)
|
||||
j -= inc;
|
||||
if (j <= inc) break;
|
||||
flag = 0;
|
||||
if (list[j-inc-1][0] > v0 ||
|
||||
(list[j-inc-1][0] == v0 && list[j-inc-1][1] > v1)) flag = 1;
|
||||
if (list[j - inc - 1][0] > v0 || (list[j - inc - 1][0] == v0 && list[j - inc - 1][1] > v1))
|
||||
flag = 1;
|
||||
}
|
||||
list[j - 1][0] = v0;
|
||||
list[j - 1][1] = v1;
|
||||
@ -1289,17 +1245,23 @@ int FixPOEMS::loopcheck(int nvert, int nedge, tagint **elist)
|
||||
and divide by principal moments
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixPOEMS::omega_from_mq(double *m, double *ex, double *ey, double *ez,
|
||||
double *inertia, double *w)
|
||||
void FixPOEMS::omega_from_mq(double *m, double *ex, double *ey, double *ez, double *inertia,
|
||||
double *w)
|
||||
{
|
||||
double wbody[3];
|
||||
|
||||
if (inertia[0] == 0.0) wbody[0] = 0.0;
|
||||
else wbody[0] = (m[0]*ex[0] + m[1]*ex[1] + m[2]*ex[2]) / inertia[0];
|
||||
if (inertia[1] == 0.0) wbody[1] = 0.0;
|
||||
else wbody[1] = (m[0]*ey[0] + m[1]*ey[1] + m[2]*ey[2]) / inertia[1];
|
||||
if (inertia[2] == 0.0) wbody[2] = 0.0;
|
||||
else wbody[2] = (m[0]*ez[0] + m[1]*ez[1] + m[2]*ez[2]) / inertia[2];
|
||||
if (inertia[0] == 0.0)
|
||||
wbody[0] = 0.0;
|
||||
else
|
||||
wbody[0] = (m[0] * ex[0] + m[1] * ex[1] + m[2] * ex[2]) / inertia[0];
|
||||
if (inertia[1] == 0.0)
|
||||
wbody[1] = 0.0;
|
||||
else
|
||||
wbody[1] = (m[0] * ey[0] + m[1] * ey[1] + m[2] * ey[2]) / inertia[1];
|
||||
if (inertia[2] == 0.0)
|
||||
wbody[2] = 0.0;
|
||||
else
|
||||
wbody[2] = (m[0] * ez[0] + m[1] * ez[1] + m[2] * ez[2]) / inertia[2];
|
||||
|
||||
w[0] = wbody[0] * ex[0] + wbody[1] * ey[0] + wbody[2] * ez[0];
|
||||
w[1] = wbody[0] * ex[1] + wbody[1] * ey[1] + wbody[2] * ez[1];
|
||||
@ -1357,22 +1319,16 @@ void FixPOEMS::set_xv()
|
||||
// x = displacement from center-of-mass, based on body orientation
|
||||
// v = vcm + omega around center-of-mass
|
||||
|
||||
x[i][0] = ex_space[ibody][0]*displace[i][0] +
|
||||
ey_space[ibody][0]*displace[i][1] +
|
||||
x[i][0] = ex_space[ibody][0] * displace[i][0] + ey_space[ibody][0] * displace[i][1] +
|
||||
ez_space[ibody][0] * displace[i][2];
|
||||
x[i][1] = ex_space[ibody][1]*displace[i][0] +
|
||||
ey_space[ibody][1]*displace[i][1] +
|
||||
x[i][1] = ex_space[ibody][1] * displace[i][0] + ey_space[ibody][1] * displace[i][1] +
|
||||
ez_space[ibody][1] * displace[i][2];
|
||||
x[i][2] = ex_space[ibody][2]*displace[i][0] +
|
||||
ey_space[ibody][2]*displace[i][1] +
|
||||
x[i][2] = ex_space[ibody][2] * displace[i][0] + ey_space[ibody][2] * displace[i][1] +
|
||||
ez_space[ibody][2] * displace[i][2];
|
||||
|
||||
v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] +
|
||||
vcm[ibody][0];
|
||||
v[i][1] = omega[ibody][2]*x[i][0] - omega[ibody][0]*x[i][2] +
|
||||
vcm[ibody][1];
|
||||
v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] +
|
||||
vcm[ibody][2];
|
||||
v[i][0] = omega[ibody][1] * x[i][2] - omega[ibody][2] * x[i][1] + vcm[ibody][0];
|
||||
v[i][1] = omega[ibody][2] * x[i][0] - omega[ibody][0] * x[i][2] + vcm[ibody][1];
|
||||
v[i][2] = omega[ibody][0] * x[i][1] - omega[ibody][1] * x[i][0] + vcm[ibody][2];
|
||||
|
||||
// add center of mass to displacement
|
||||
// map back into periodic box via xbox,ybox,zbox
|
||||
@ -1437,14 +1393,11 @@ void FixPOEMS::set_v()
|
||||
if (natom2body[i] == 0) continue;
|
||||
ibody = atom2body[i][0];
|
||||
|
||||
dx = ex_space[ibody][0]*displace[i][0] +
|
||||
ey_space[ibody][0]*displace[i][1] +
|
||||
dx = ex_space[ibody][0] * displace[i][0] + ey_space[ibody][0] * displace[i][1] +
|
||||
ez_space[ibody][0] * displace[i][2];
|
||||
dy = ex_space[ibody][1]*displace[i][0] +
|
||||
ey_space[ibody][1]*displace[i][1] +
|
||||
dy = ex_space[ibody][1] * displace[i][0] + ey_space[ibody][1] * displace[i][1] +
|
||||
ez_space[ibody][1] * displace[i][2];
|
||||
dz = ex_space[ibody][2]*displace[i][0] +
|
||||
ey_space[ibody][2]*displace[i][1] +
|
||||
dz = ex_space[ibody][2] * displace[i][0] + ey_space[ibody][2] * displace[i][1] +
|
||||
ez_space[ibody][2] * displace[i][2];
|
||||
|
||||
// save old velocities for virial
|
||||
@ -1536,8 +1489,7 @@ int FixPOEMS::pack_exchange(int i, double *buf)
|
||||
{
|
||||
int m = 0;
|
||||
buf[m++] = static_cast<double>(natom2body[i]);
|
||||
for (int j = 0; j < natom2body[i]; j++)
|
||||
buf[m++] = static_cast<double> (atom2body[i][j]);
|
||||
for (int j = 0; j < natom2body[i]; j++) buf[m++] = static_cast<double>(atom2body[i][j]);
|
||||
buf[m++] = displace[i][0];
|
||||
buf[m++] = displace[i][1];
|
||||
buf[m++] = displace[i][2];
|
||||
@ -1552,8 +1504,7 @@ int FixPOEMS::unpack_exchange(int nlocal, double *buf)
|
||||
{
|
||||
int m = 0;
|
||||
natom2body[nlocal] = static_cast<int>(buf[m++]);
|
||||
for (int i = 0; i < natom2body[nlocal]; i++)
|
||||
atom2body[nlocal][i] = static_cast<int> (buf[m++]);
|
||||
for (int i = 0; i < natom2body[nlocal]; i++) atom2body[nlocal][i] = static_cast<int>(buf[m++]);
|
||||
displace[nlocal][0] = buf[m++];
|
||||
displace[nlocal][1] = buf[m++];
|
||||
displace[nlocal][2] = buf[m++];
|
||||
@ -1566,9 +1517,12 @@ int FixPOEMS::modify_param(int narg, char **arg)
|
||||
{
|
||||
if (strcmp(arg[0], "bodyforces") == 0) {
|
||||
if (narg < 2) error->all(FLERR, "Illegal fix_modify command");
|
||||
if (strcmp(arg[1],"early") == 0) earlyflag = 1;
|
||||
else if (strcmp(arg[1],"late") == 0) earlyflag = 0;
|
||||
else error->all(FLERR,"Illegal fix_modify command");
|
||||
if (strcmp(arg[1], "early") == 0)
|
||||
earlyflag = 1;
|
||||
else if (strcmp(arg[1], "late") == 0)
|
||||
earlyflag = 0;
|
||||
else
|
||||
error->all(FLERR, "Illegal fix_modify command");
|
||||
return 2;
|
||||
}
|
||||
|
||||
|
||||
@ -53,7 +53,6 @@ class FixPOEMS : public Fix {
|
||||
void reset_dt() override;
|
||||
|
||||
private:
|
||||
int me;
|
||||
double dtv, dtf, dthalf;
|
||||
double *step_respa;
|
||||
int nlevels_respa;
|
||||
@ -101,8 +100,7 @@ class FixPOEMS : public Fix {
|
||||
// internal class functions
|
||||
|
||||
void compute_forces_and_torques();
|
||||
void readfile(char *);
|
||||
int readline(FILE *, char **, int *);
|
||||
void readfile(const char *);
|
||||
void jointbuild();
|
||||
void sortlist(int, tagint **);
|
||||
int loopcheck(int, int, tagint **);
|
||||
|
||||
Reference in New Issue
Block a user