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Revert "use neighbor list exclusions instead of a zero cutoff" 

This reverts commit bbb4d63db9.
This commit is contained in:
Axel Kohlmeyer 2017-07-18 01:17:34 -04:00
parent bc5186bc30
commit d9186c8fde
2 changed files with 140 additions and 142 deletions
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139
examples/ASPHERE/poly/in.poly
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@ -1,115 +1,114 @@
# SRD diffusion demo - poydisperse spheres # SRD diffusion demo - poydisperse spheres
units lj units lj
atom_style sphere atom_style sphere
atom_modify first big atom_modify first big
dimension 2 dimension 2
# create big particles with 3 different types and diameters # create big particles with 3 different types and diameters
lattice sq 0.3 lattice sq 0.3
region box block 0 10 0 10 -0.5 0.5 region box block 0 10 0 10 -0.5 0.5
create_box 4 box create_box 4 box
create_atoms 1 region box create_atoms 1 region box
group big type 1 group big type 1
set group big type/fraction 2 0.33 394895 set group big type/fraction 2 0.33 394895
set group big type/fraction 3 0.5 989894 set group big type/fraction 3 0.5 989894
group big type 2 3 group big type 2 3
set type 1*3 mass 1.0 set type 1*3 mass 1.0
velocity big create 1.44 87287 loop geom velocity big create 1.44 87287 loop geom
# equilibrate big particles, repulsive only to prevent aggregation # equilibrate big particles, repulsive only to prevent aggregation
pair_style lj/cut 1.12 pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12 pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24 pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68 pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.1 pair_coeff 4 4 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin fix 1 big nve
neigh_modify delay 0 every 1 check yes fix 2 all enforce2d
neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4
fix 1 big nve #dump 1 all atom 10 dump.poly.equil
fix 2 all enforce2d
#dump 1 all atom 10 dump.poly.equil run 1000
run 1000 #undump 1
unfix 1
#undump 1 unfix 2
unfix 1
unfix 2
# add small particles as hi density lattice # add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 250.0 lattice sq 250.0
create_atoms 4 region plane create_atoms 4 region plane
set type 4 mass 0.1 set type 4 mass 0.1
group small type 4 group small type 4
velocity small create 1.0 593849 loop geom velocity small create 1.0 593849 loop geom
# delete overlaps # delete overlaps
# must set *-4 cutoffs to non-zero values # must set *-4 cutoffs to non-zero values
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.0 2.0 pair_coeff 2 2 1.0 2.0
pair_coeff 3 3 1.0 1.5 pair_coeff 3 3 1.0 1.5
pair_coeff 4 4 0.0 1.0 0.1 pair_coeff 1 4 0.0 1.0 0.5
neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4 pair_coeff 2 4 0.0 1.0 1.0
pair_coeff 3 4 0.0 1.0 0.75
pair_coeff 4 4 0.0 1.0 0.0
delete_atoms overlap 1.0 small big delete_atoms overlap 1.0 small big
# SRD run # SRD run
reset_timestep 0 reset_timestep 0
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes comm_modify mode multi group big vel yes
neigh_modify include big neigh_modify include big
# no pairwise interactions with small particles # no pairwise interactions with small particles
pair_style lj/cut 1.12 pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12 pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24 pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68 pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.1 pair_coeff 4 4 0.0 1.0 0.0
neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4
# use fix SRD to push small particles out from inside big ones # use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles # if comment out, big particles won't see SRD particles
timestep 0.001 timestep 0.001
fix 1 big nve fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
search 0.2 inside ignore search 0.2 inside ignore
fix 3 all enforce2d fix 3 all enforce2d
# diagnostics # diagnostics
compute tbig big temp/sphere compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big) variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big) variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press & thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
thermo_modify temp tbig thermo_modify temp tbig
thermo 1000 thermo 1000
#dump 1 all atom 1000 dump.poly #dump 1 all atom 1000 dump.poly
#dump 1 all image 1000 image.*.jpg type type zoom 1.6 #dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1 #dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
run 100000 run 100000

143
examples/ASPHERE/poly/in.poly.mp
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@ -1,116 +1,115 @@
# SRD viscosity demo - poydisperse spheres # SRD viscosity demo - poydisperse spheres
units lj units lj
atom_style sphere atom_style sphere
atom_modify first big atom_modify first big
dimension 2 dimension 2
# create big particles with 3 different types and diameters # create big particles with 3 different types and diameters
lattice sq 0.3 lattice sq 0.3
region box block 0 10 0 10 -0.5 0.5 region box block 0 10 0 10 -0.5 0.5
create_box 4 box create_box 4 box
create_atoms 1 region box create_atoms 1 region box
group big type 1 group big type 1
set group big type/fraction 2 0.33 394895 set group big type/fraction 2 0.33 394895
set group big type/fraction 3 0.5 989894 set group big type/fraction 3 0.5 989894
group big type 2 3 group big type 2 3
set type 1*3 mass 1.0 set type 1*3 mass 1.0
velocity big create 1.44 87287 loop geom velocity big create 1.44 87287 loop geom
# equilibrate big particles, repulsive only to prevent aggregation # equilibrate big particles, repulsive only to prevent aggregation
pair_style lj/cut 1.12 pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12 pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24 pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68 pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.1 pair_coeff 4 4 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin fix 1 big nve
neigh_modify delay 0 every 1 check yes fix 2 all enforce2d
neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4
fix 1 big nve #dump 1 all atom 10 dump.poly.equil
fix 2 all enforce2d
#dump 1 all atom 10 dump.poly.equil run 1000
run 1000 #undump 1
unfix 1
#undump 1 unfix 2
unfix 1
unfix 2
# add small particles as hi density lattice # add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 250.0 lattice sq 250.0
create_atoms 4 region plane create_atoms 4 region plane
set type 4 mass 0.1 set type 4 mass 0.1
group small type 4 group small type 4
velocity small create 1.0 593849 loop geom velocity small create 1.0 593849 loop geom
# delete overlaps # delete overlaps
# must set *-4 cutoffs to non-zero values # must set *-4 cutoffs to non-zero values
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.0 2.0 pair_coeff 2 2 1.0 2.0
pair_coeff 3 3 1.0 1.5 pair_coeff 3 3 1.0 1.5
pair_coeff 4 4 0.0 1.0 0.1 pair_coeff 1 4 0.0 1.0 0.5
neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4 pair_coeff 2 4 0.0 1.0 1.0
pair_coeff 3 4 0.0 1.0 0.75
pair_coeff 4 4 0.0 1.0 0.0
delete_atoms overlap 1.0 small big delete_atoms overlap 1.0 small big
# SRD run # SRD run
reset_timestep 0 reset_timestep 0
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes comm_modify mode multi group big vel yes
neigh_modify include big neigh_modify include big
# no pairwise interactions with small particles # no pairwise interactions with small particles
pair_style lj/cut 1.12 pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12 pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24 pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68 pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.1 pair_coeff 4 4 0.0 1.0 0.0
neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4
# use fix SRD to push small particles out from inside big ones # use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles # if comment out, big particles won't see SRD particles
timestep 0.001 timestep 0.001
fix 1 big nve fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
search 0.2 inside ignore search 0.2 inside ignore
fix 3 small viscosity 10 x y 50 fix 3 small viscosity 10 x y 50
fix 4 all enforce2d fix 4 all enforce2d
# diagnostics # diagnostics
compute tbig big temp/sphere compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big) variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big) variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press & thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
thermo_modify temp tbig thermo_modify temp tbig
thermo 1000 thermo 1000
#dump 1 all atom 500 dump.poly.mp #dump 1 all atom 500 dump.poly.mp
#dump 1 all image 500 image.*.jpg type type zoom 1.6 #dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1 #dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
run 50000 run 50000