diff --git a/examples/rigid/bodies.txt b/examples/rigid/bodies.txt new file mode 100644 index 0000000000..ddca2c7539 --- /dev/null +++ b/examples/rigid/bodies.txt @@ -0,0 +1,83 @@ +81 +1 1 +2 1 +3 1 +4 1 +5 1 +6 1 +7 1 +8 1 +9 1 +10 2 +11 2 +12 2 +13 2 +14 2 +15 2 +16 2 +17 2 +18 2 +19 3 +20 3 +21 3 +22 3 +23 3 +24 3 +25 3 +26 3 +27 3 +28 4 +29 4 +30 4 +31 4 +32 4 +33 4 +34 4 +35 4 +36 4 +37 5 +38 5 +39 5 +40 5 +41 5 +42 5 +43 5 +44 5 +45 5 +46 6 +47 6 +48 6 +49 6 +50 6 +51 6 +52 6 +53 6 +54 6 +55 7 +56 7 +57 7 +58 7 +59 7 +60 7 +61 7 +62 7 +63 7 +64 8 +65 8 +66 8 +67 8 +68 8 +69 8 +70 8 +71 8 +72 8 +73 9 +74 9 +75 9 +76 9 +77 9 +78 9 +79 9 +80 9 +81 9 + diff --git a/examples/rigid/data.rigid-property b/examples/rigid/data.rigid-property new file mode 100644 index 0000000000..66fc42d2d2 --- /dev/null +++ b/examples/rigid/data.rigid-property @@ -0,0 +1,185 @@ +# LAMMPS data file for rigid bodies + +81 atoms +1 atom types + +-12 12 xlo xhi +-12 12 ylo yhi +-12 12 zlo zhi + +Masses + +1 1 + +Pair Coeffs + +1 1 1 + +Atoms + +1 1 0 0 0 +2 1 0 1 0 +3 1 0 0.5 0 +4 1 0.5 0 0 +5 1 0.5 0.5 1 +6 1 1 0.5 0 +7 1 0.5 1 0 +8 1 1 0 0 +9 1 1 1 0 +10 1 2 1 0 +11 1 1 2 0 +12 1 1.5 2 0 +13 1 1.5 1 0 +14 1 1 1.5 0 +15 1 1.5 1.5 1 +16 1 2 1.5 0 +17 1 2 2 0 +18 1 2 3 0 +19 1 2 2.5 0 +20 1 2.5 2 0 +21 1 2.5 2.5 1 +22 1 3 2.5 0 +23 1 2.5 3 0 +24 1 3 2 0 +25 1 3 3 0 +26 1 4 3 0 +27 1 3 4 0 +28 1 3.5 4 0 +29 1 3.5 3 0 +30 1 3 3.5 0 +31 1 3.5 3.5 1 +32 1 4 3.5 0 +33 1 4 4 0 +34 1 4 5 0 +35 1 4 4.5 0 +36 1 4.5 4 0 +37 1 4.5 4.5 1 +38 1 5 4.5 0 +39 1 4.5 5 0 +40 1 5 4 0 +41 1 5 5 0 +42 1 6 5 0 +43 1 5 6 0 +44 1 5.5 6 0 +45 1 5.5 5 0 +46 1 5 5.5 0 +47 1 5.5 5.5 1 +48 1 6 5.5 0 +49 1 6 6 0 +50 1 6 7 0 +51 1 6 6.5 0 +52 1 6.5 6 0 +53 1 6.5 6.5 1 +54 1 7 6.5 0 +55 1 6.5 7 0 +56 1 7 6 0 +57 1 7 7 0 +58 1 8 7 0 +59 1 7 8 0 +60 1 7.5 8 0 +61 1 7.5 7 0 +62 1 7 7.5 0 +63 1 7.5 7.5 1 +64 1 8 7.5 0 +65 1 8 8 0 +66 1 8 9 0 +67 1 8 8.5 0 +68 1 8.5 8 0 +69 1 8.5 8.5 1 +70 1 9 8.5 0 +71 1 8.5 9 0 +72 1 9 8 0 +73 1 9 9 0 +74 1 10 9 0 +75 1 9 10 0 +76 1 9.5 10 0 +77 1 9.5 9 0 +78 1 9 9.5 0 +79 1 9.5 9.5 1 +80 1 10 9.5 0 +81 1 10 10 0 + +Bodies + +1 1 +2 1 +3 1 +4 1 +5 1 +6 1 +7 1 +8 1 +9 1 +10 2 +11 2 +12 2 +13 2 +14 2 +15 2 +16 2 +17 2 +18 2 +19 3 +20 3 +21 3 +22 3 +23 3 +24 3 +25 3 +26 3 +27 3 +28 4 +29 4 +30 4 +31 4 +32 4 +33 4 +34 4 +35 4 +36 4 +37 5 +38 5 +39 5 +40 5 +41 5 +42 5 +43 5 +44 5 +45 5 +46 6 +47 6 +48 6 +49 6 +50 6 +51 6 +52 6 +53 6 +54 6 +55 7 +56 7 +57 7 +58 7 +59 7 +60 7 +61 7 +62 7 +63 7 +64 8 +65 8 +66 8 +67 8 +68 8 +69 8 +70 8 +71 8 +72 8 +73 9 +74 9 +75 9 +76 9 +77 9 +78 9 +79 9 +80 9 +81 9 + diff --git a/examples/rigid/in.rigid-atomfile b/examples/rigid/in.rigid-atomfile new file mode 100644 index 0000000000..8817386c79 --- /dev/null +++ b/examples/rigid/in.rigid-atomfile @@ -0,0 +1,83 @@ +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid + +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 + +variable bodies atomfile bodies.txt +fix 1 all rigid custom v_bodies + +# 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 +#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 + +#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 diff --git a/examples/rigid/in.rigid-atomvar b/examples/rigid/in.rigid-atomvar new file mode 100644 index 0000000000..994ab1d284 --- /dev/null +++ b/examples/rigid/in.rigid-atomvar @@ -0,0 +1,83 @@ +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid + +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 + +variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) +fix 1 all rigid custom v_bodies + +# 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 +#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 + +#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 diff --git a/examples/rigid/in.rigid-property b/examples/rigid/in.rigid-property new file mode 100644 index 0000000000..53d62776e6 --- /dev/null +++ b/examples/rigid/in.rigid-property @@ -0,0 +1,85 @@ +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +fix 0 all property/atom i_bodies + +read_data data.rigid-property fix 0 NULL Bodies + +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 + +# assemble bodies from per-atom custom integer property bodies +fix 1 all rigid custom i_bodies + +# 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 +#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 + +#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