Merge branch 'develop' into general-triclinic
# Conflicts: # src/atom.cpp
This commit is contained in:
Axel Kohlmeyer
@ -1,104 +1,104 @@
|
||||
# SRD diffusion demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
delete_atoms overlap 0.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.dimer
|
||||
#dump 1 all atom 1000 dump.dimer
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
run 10000
|
||||
|
||||
@ -1,105 +1,105 @@
|
||||
# SRD viscosity demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
delete_atoms overlap 0.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.dimer.mp
|
||||
#dump 1 all atom 500 dump.dimer.mp
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 50000
|
||||
run 25000
|
||||
|
||||
@ -1,286 +0,0 @@
|
||||
LAMMPS (1 Feb 2014)
|
||||
# SRD diffusion demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
200 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
200 settings made for mass
|
||||
group big type 1
|
||||
200 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 3.1029 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.4028231 0 0 0.83369167 -0.55065517
|
||||
100 9.5167872 2.392105 0 4.7237178 2.8319556
|
||||
200 13.564465 3.0352634 0 6.3585572 3.6388732
|
||||
300 13.133051 4.3835112 0 7.6011086 4.060051
|
||||
400 14.584346 5.5141254 0 9.0872901 4.4231056
|
||||
500 15.331515 6.6554832 0 10.411704 4.847642
|
||||
600 16.953755 7.4794317 0 11.633102 5.2020696
|
||||
700 16.503256 8.8572339 0 12.900532 5.6694613
|
||||
800 17.006131 9.877343 0 14.043845 5.5483363
|
||||
900 17.305927 11.081594 0 15.321546 6.2908201
|
||||
1000 18.122491 12.126462 0 16.566472 5.7536055
|
||||
Loop time of 0.185949 on 8 procs for 1000 steps with 200 atoms
|
||||
|
||||
Pair time (%) = 0.00187448 (1.00806)
|
||||
Neigh time (%) = 0.000561714 (0.30208)
|
||||
Comm time (%) = 0.0652371 (35.0833)
|
||||
Outpt time (%) = 0.00209856 (1.12857)
|
||||
Other time (%) = 0.116177 (62.4779)
|
||||
|
||||
Nlocal: 25 ave 30 max 20 min
|
||||
Histogram: 1 0 1 1 0 0 3 1 0 1
|
||||
Nghost: 28.375 ave 36 max 22 min
|
||||
Histogram: 1 0 1 2 1 0 2 0 0 1
|
||||
Neighs: 33.125 ave 45 max 22 min
|
||||
Histogram: 1 0 2 1 0 1 1 0 1 1
|
||||
|
||||
Total # of neighbors = 265
|
||||
Ave neighs/atom = 1.325
|
||||
Neighbor list builds = 99
|
||||
Dangerous builds = 96
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 29929 atoms
|
||||
|
||||
set type 2 mass 0.1
|
||||
29929 settings made for mass
|
||||
group small type 2
|
||||
29929 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
Deleted 12759 atoms, new total = 17370
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.dimer
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 17170 200
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 75 75 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
|
||||
SRD per actual grid cell = 5.5499
|
||||
SRD viscosity = 0.235551
|
||||
big/SRD mass density ratio = 0.142367
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.20347 7.72323
|
||||
ave/max big velocity = 2.64047 6.60911
|
||||
Memory usage per processor = 7.0395 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 6.9744766 0 0.30175295 21.011259 26.207244 2.7219331 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.1941672 3369 0.24718395 20.578272 21.467926 9.8944086 13658 56 56 2 664 40320 5625 3369 1.1358997 0 4 0
|
||||
2000 1.3247909 3390 0.24717547 20.48022 21.467189 6.5341926 13389 48 48 3 1988 40320 5625 3390 1.1814916 0 144 0
|
||||
3000 1.386904 3355 0.24769415 20.478993 21.512237 6.1207029 13507 45 45 0 2871 40320 5625 3355 1.1657697 0 144 0
|
||||
4000 1.1567347 3376 0.24573733 20.48052 21.342287 3.5540965 13475 46 46 0 3731 40320 5625 3376 1.1485984 0 144 0
|
||||
5000 1.2565155 3376 0.24620928 20.447172 21.383276 2.5808161 13267 55 55 0 4559 40320 5625 3376 1.1778096 0 144 0
|
||||
6000 1.1489985 3375 0.24520477 20.440031 21.296035 7.8204262 13362 59 59 0 5354 40320 5625 3375 1.1530517 0 144 0
|
||||
7000 1.1608248 3399 0.24587989 20.489854 21.354669 7.9622779 13333 59 59 2 6254 40320 5625 3399 1.1809325 0 144 0
|
||||
8000 1.1749441 3374 0.24700359 20.576929 21.452262 6.7498405 13495 64 64 0 7134 40320 5625 3374 1.1445035 0 144 0
|
||||
9000 1.1285085 3405 0.24536183 20.468936 21.309675 5.8959937 13333 60 60 0 8008 40320 5625 3405 1.162836 0 144 0
|
||||
10000 1.1462675 3425 0.24564758 20.480523 21.334492 7.0047543 13487 45 45 0 8967 40320 5625 3425 1.1881074 0 144 0
|
||||
11000 1.2854766 3388 0.246088 20.415062 21.372742 7.8508136 13491 60 60 1 9833 40320 5625 3388 1.1698514 0 144 0
|
||||
12000 1.2926536 3360 0.24602616 20.404345 21.367372 7.9286141 13142 64 64 1 11029 40320 5625 3360 1.1658039 0 161 0
|
||||
13000 1.2289767 3412 0.24595657 20.44574 21.361328 2.2809592 13162 56 56 1 12018 40320 5625 3412 1.1665531 0 161 0
|
||||
14000 1.3518235 3380 0.24629055 20.383226 21.390334 8.0062608 13310 59 59 7 13146 40320 5625 3380 1.1733296 0 161 0
|
||||
15000 1.2971143 3355 0.24671134 20.46053 21.42688 9.7871945 12967 60 60 3 14084 40320 5625 3355 1.1703643 0 161 0
|
||||
16000 1.4160948 3384 0.2478594 20.471598 21.526589 7.3141215 13123 56 56 1 14929 40320 5625 3384 1.1666782 0 161 0
|
||||
17000 1.3172038 3391 0.247377 20.503375 21.484692 6.1541908 12957 54 54 0 15778 40320 5625 3391 1.1639931 0 161 0
|
||||
18000 0.98748293 3369 0.2443499 20.486114 21.221789 4.0981146 13355 50 50 1 17031 40320 5625 3369 1.2083414 0 192 0
|
||||
19000 1.4619261 3367 0.24867817 20.508564 21.597699 11.68547 13519 58 58 0 18334 40320 5625 3367 1.1667505 0 192 0
|
||||
20000 1.44087 3391 0.24747923 20.420123 21.493571 4.0409936 13594 67 67 0 19303 40320 5625 3391 1.1869387 0 192 0
|
||||
21000 1.1155365 3377 0.24474418 20.424957 21.256032 8.4985692 13423 52 52 0 20245 40320 5625 3377 1.1726608 0 192 0
|
||||
22000 1.2045785 3382 0.24466159 20.351448 21.248859 7.0518674 13271 62 62 0 21128 40320 5625 3382 1.1658557 0 192 0
|
||||
23000 1.2634616 3378 0.24571326 20.398918 21.340197 6.8382109 13246 61 61 1 22067 40320 5625 3378 1.170196 0 192 0
|
||||
24000 1.365723 3375 0.24749053 20.477089 21.494552 5.9584152 13017 46 46 1 23017 40320 5625 3375 1.1841192 0 192 0
|
||||
25000 1.1421045 3367 0.24497142 20.4249 21.275768 10.381661 13049 66 66 1 23907 40320 5625 3367 1.1856767 0 192 0
|
||||
26000 1.4008939 3340 0.24678624 20.389719 21.433385 7.3799658 12971 53 53 5 24850 40320 5625 3340 1.1713233 0 192 0
|
||||
27000 1.1835022 3379 0.24522732 20.416284 21.297993 7.2251705 12717 46 46 1 25723 40320 5625 3379 1.1798333 0 192 0
|
||||
28000 1.0496668 3398 0.24461816 20.463086 21.245087 6.5485338 13385 60 60 0 26990 40320 5625 3398 1.1765205 0 192 0
|
||||
29000 1.1779927 3453 0.24501083 20.401586 21.27919 4.8540048 13157 77 77 2 28023 40320 5625 3453 1.1741595 0 192 0
|
||||
30000 1.2277637 3375 0.24554215 20.410652 21.325336 10.087705 12939 72 72 1 28855 40320 5625 3375 1.1627414 0 192 0
|
||||
31000 1.1575066 3397 0.24504213 20.419566 21.281909 6.4849648 12977 66 66 0 29745 40320 5625 3397 1.1575018 0 192 0
|
||||
32000 1.1752733 3381 0.2451073 20.41199 21.287569 7.2784509 12971 48 48 0 30561 40320 5625 3381 1.1790395 0 192 0
|
||||
33000 1.1743895 3370 0.24485514 20.390748 21.265669 9.084299 12810 64 64 0 31342 40320 5625 3370 1.1429061 0 192 0
|
||||
34000 1.2975876 3377 0.24608262 20.405573 21.372276 10.624304 12610 60 60 1 32140 40320 5625 3377 1.1685718 0 192 0
|
||||
35000 1.7701252 3356 0.2497356 20.370794 21.689537 7.107766 12983 45 45 8 33862 40320 5625 3356 1.1720964 0 242 0
|
||||
36000 1.2711521 3393 0.24675748 20.483878 21.430887 8.7087273 13175 60 60 0 34920 40320 5625 3393 1.1796212 0 242 0
|
||||
37000 1.1140649 3373 0.24450996 20.405711 21.23569 8.0025138 12964 50 50 1 35770 40320 5625 3373 1.1772234 0 242 0
|
||||
38000 1.3128798 3379 0.24583813 20.372946 21.351041 5.0554655 12939 56 56 1 36679 40320 5625 3379 1.1702949 0 242 0
|
||||
39000 1.2093703 3365 0.24536578 20.409037 21.310018 5.6243735 12873 62 62 3 37511 40320 5625 3365 1.1751064 0 242 0
|
||||
40000 1.2095402 3365 0.24485106 20.364207 21.265315 3.9565189 12876 54 54 1 38503 40320 5625 3365 1.1637516 0 242 0
|
||||
41000 1.1146238 3350 0.24476111 20.427107 21.257502 6.5033046 12656 53 53 0 39313 40320 5625 3350 1.1553197 0 242 0
|
||||
42000 1.2302245 3370 0.24452048 20.320087 21.236604 10.7363 12676 52 52 1 40108 40320 5625 3370 1.1492163 0 242 0
|
||||
43000 1.2749689 3404 0.24511103 20.338041 21.287893 9.18604 13057 72 72 1 41014 40320 5625 3404 1.1572511 0 242 0
|
||||
44000 1.1989211 3385 0.24450633 20.342179 21.235375 7.6714085 13086 52 53 1 41840 40320 5625 3385 1.1530041 0 242 0
|
||||
45000 1.6465972 3370 0.249994 20.485264 21.711979 7.4908607 12894 58 58 7 43545 40320 5625 3370 1.1978571 0 361 0
|
||||
46000 1.3082316 3412 0.24665637 20.447473 21.422106 8.9900563 13136 53 53 4 44510 40320 5625 3412 1.1686573 0 361 0
|
||||
47000 1.2163258 3355 0.24493724 20.366636 21.272799 6.9309438 13020 56 56 0 45414 40320 5625 3355 1.1620943 0 361 0
|
||||
48000 1.349966 3362 0.24683156 20.431596 21.437321 8.8527164 13044 64 64 1 46260 40320 5625 3362 1.1683452 0 361 0
|
||||
49000 1.3903769 3347 0.24726403 20.439051 21.474881 5.9250552 13103 58 59 2 49229 40320 5625 3347 1.1924538 0 578 0
|
||||
50000 1.2737918 3349 0.24563843 20.384723 21.333698 7.2419874 12892 41 41 1 50225 40320 5625 3349 1.1803233 0 578 0
|
||||
51000 1.2229799 3355 0.24504936 20.371417 21.282537 8.5556146 12912 63 63 0 51096 40320 5625 3355 1.1333843 0 578 0
|
||||
52000 1.2326547 3386 0.24596384 20.443632 21.361959 6.1757404 12790 66 66 1 52114 40320 5625 3386 1.1685608 0 578 0
|
||||
53000 1.3695441 3389 0.24696147 20.428294 21.448604 8.7464732 12997 60 60 1 53115 40320 5625 3389 1.1631228 0 578 0
|
||||
54000 1.0711204 3400 0.24322154 20.325806 21.12379 8.7228921 13005 56 56 0 53913 40320 5625 3400 1.1250986 0 578 0
|
||||
55000 1.3412565 3360 0.24617922 20.381429 21.380665 6.9489559 12960 46 46 0 55249 40320 5625 3360 1.176467 0 578 0
|
||||
56000 1.3910761 3355 0.2467942 20.397725 21.434077 6.6762734 12966 65 65 2 56653 40320 5625 3355 1.1715559 0 578 0
|
||||
57000 1.1177307 3388 0.24424738 20.380176 21.212885 5.5073089 13153 62 62 1 57550 40320 5625 3388 1.1576307 0 578 0
|
||||
58000 1.3136279 3365 0.24661231 20.439627 21.418279 9.1390284 12799 52 52 1 58366 40320 5625 3365 1.159026 0 578 0
|
||||
59000 1.2667621 3374 0.24556104 20.383238 21.326976 3.4246418 13127 54 54 1 59170 40320 5625 3374 1.1461442 0 578 0
|
||||
60000 1.1903121 3326 0.24492127 20.384629 21.271412 6.9439977 13078 47 47 2 60105 40320 5625 3326 1.1665886 0 578 0
|
||||
61000 1.209313 3362 0.2455341 20.423699 21.324637 9.1212002 13225 61 61 4 61358 40320 5625 3362 1.1725894 0 578 0
|
||||
62000 1.1720074 3366 0.24476301 20.384522 21.257667 7.7592884 13187 53 54 2 62257 40320 5625 3366 1.1599665 0 578 0
|
||||
63000 1.2155508 3386 0.24486685 20.361101 21.266686 5.7864126 13090 42 42 0 63137 40320 5625 3386 1.1724234 0 578 0
|
||||
64000 1.1967326 3379 0.2451834 20.402613 21.294179 4.8815049 13033 48 48 4 64152 40320 5625 3379 1.1818756 0 578 0
|
||||
65000 1.1732378 3386 0.24500733 20.404824 21.278887 11.381026 12998 59 59 0 65071 40320 5625 3386 1.1625543 0 578 0
|
||||
66000 1.1960739 3385 0.24407516 20.306852 21.197927 12.17249 12994 61 61 0 65941 40320 5625 3385 1.1826516 0 578 0
|
||||
67000 1.3468331 3366 0.24657491 20.41164 21.415031 7.8115623 12894 62 62 1 66788 40320 5625 3366 1.1750424 0 578 0
|
||||
68000 1.0742924 3369 0.24347736 20.345661 21.146009 9.5240252 13065 68 68 2 67665 40320 5625 3369 1.1561575 0 578 0
|
||||
69000 1.1411254 3380 0.2450544 20.432836 21.282975 8.0392218 13134 49 49 1 68471 40320 5625 3380 1.1405485 0 578 0
|
||||
70000 1.1585312 3388 0.24435206 20.358871 21.221977 7.5303626 13113 59 59 0 69320 40320 5625 3388 1.1726416 0 578 0
|
||||
71000 1.3418857 3382 0.24598802 20.364355 21.36406 9.2840877 13265 68 68 0 70522 40320 5625 3382 1.1696767 0 578 0
|
||||
72000 1.1547857 3388 0.24328952 20.26938 21.129695 7.9643121 13270 50 50 1 71384 40320 5625 3388 1.1647353 0 578 0
|
||||
73000 1.1114283 3385 0.24397276 20.36102 21.189034 13.168935 13110 62 62 0 72335 40320 5625 3385 1.1625358 0 578 0
|
||||
74000 1.6120075 3370 0.25009739 20.520013 21.720959 12.065782 12902 51 51 9 73743 40320 5625 3370 1.1873738 0 578 0
|
||||
75000 1.3271087 3353 0.24600453 20.376798 21.365493 7.5902315 13076 51 51 1 74746 40320 5625 3353 1.1706259 0 578 0
|
||||
76000 1.1908626 3386 0.2451628 20.405197 21.292389 6.8084086 13124 58 58 1 75702 40320 5625 3386 1.1765809 0 578 0
|
||||
77000 1.042536 3391 0.24320847 20.345966 21.122655 6.4883579 12846 57 57 0 76930 40320 5625 3391 1.1769829 0 578 0
|
||||
78000 1.3791243 3355 0.24628683 20.362563 21.390011 9.2397346 12897 56 56 12 78068 40320 5625 3355 1.1905167 0 578 0
|
||||
79000 1.2058397 3391 0.2453076 20.406614 21.304965 9.7949819 13020 51 51 1 79065 40320 5625 3391 1.1777257 0 578 0
|
||||
80000 1.0634737 3383 0.24440921 20.434652 21.22694 7.5296946 12973 61 61 2 80029 40320 5625 3383 1.1648017 0 578 0
|
||||
81000 1.3768966 3373 0.24730623 20.452758 21.478546 7.1508584 13297 56 56 1 81172 40320 5625 3373 1.1740603 0 578 0
|
||||
82000 1.3348382 3375 0.24680945 20.440946 21.4354 9.3251946 12822 56 56 2 82447 40320 5625 3375 1.1573749 0 578 0
|
||||
83000 1.2042501 3393 0.24484972 20.368032 21.265198 7.5283729 12990 51 51 0 83344 40320 5625 3393 1.1833162 0 578 0
|
||||
84000 1.1985223 3405 0.24537841 20.418216 21.311115 7.848856 13189 60 60 0 84147 40320 5625 3405 1.173911 0 578 0
|
||||
85000 1.1811593 3391 0.24418657 20.32764 21.207604 8.3169438 13303 51 51 0 85022 40320 5625 3391 1.1586027 0 578 0
|
||||
86000 1.2595689 3385 0.24556774 20.389179 21.327558 8.3808674 12966 56 56 1 85962 40320 5625 3385 1.1617838 0 578 0
|
||||
87000 1.1419322 3356 0.24399697 20.340397 21.191137 6.8911116 13166 63 63 0 86753 40320 5625 3356 1.1729274 0 578 0
|
||||
88000 1.275219 3380 0.24586129 20.403015 21.353053 6.838563 12963 56 56 0 87729 40320 5625 3380 1.1511968 0 578 0
|
||||
89000 1.2794858 3366 0.24507826 20.33183 21.285047 9.3370019 12889 64 64 1 88575 40320 5625 3366 1.1660311 0 578 0
|
||||
90000 1.0549593 3402 0.24289618 20.309589 21.095533 4.9944605 13076 59 59 1 89560 40320 5625 3402 1.1744335 0 578 0
|
||||
91000 1.214812 3402 0.24442304 20.323106 21.228141 7.5681019 13229 44 44 1 90440 40320 5625 3402 1.1696689 0 578 0
|
||||
92000 1.2019714 3374 0.24469176 20.356011 21.25148 7.6728432 13331 64 64 2 91243 40320 5625 3374 1.1678246 0 578 0
|
||||
93000 1.0964004 3364 0.24364709 20.343931 21.16075 5.9650235 13086 55 55 0 92088 40320 5625 3364 1.1570838 0 578 0
|
||||
94000 1.1722133 3393 0.24332541 20.259513 21.132812 7.1743779 13206 66 66 0 92858 40320 5625 3393 1.154328 0 578 0
|
||||
95000 1.2413711 3373 0.24549874 20.396744 21.321566 8.131371 12967 61 61 1 93789 40320 5625 3373 1.1635681 0 578 0
|
||||
96000 1.1702409 3363 0.24528289 20.430989 21.302819 11.399295 12776 63 63 0 94571 40320 5625 3363 1.1367365 0 578 0
|
||||
97000 1.0696537 3368 0.242673 20.279258 21.07615 8.537175 13054 55 55 0 95403 40320 5625 3368 1.1648141 0 578 0
|
||||
98000 1.1635952 3369 0.24486659 20.399785 21.266664 8.6714443 12750 70 70 0 96296 40320 5625 3369 1.1686272 0 578 0
|
||||
99000 1.1286255 3397 0.24343772 20.30174 21.142566 6.7153212 12810 44 45 1 97021 40320 5625 3397 1.137818 0 578 0
|
||||
100000 1.2847818 3367 0.24509282 20.329149 21.286312 8.7486629 13260 64 64 0 97855 40320 5625 3367 1.1597138 0 578 0
|
||||
Loop time of 20.8136 on 8 procs for 100000 steps with 17370 atoms
|
||||
|
||||
Pair time (%) = 0.322913 (1.55145)
|
||||
Neigh time (%) = 1.11753 (5.36921)
|
||||
Comm time (%) = 1.72335 (8.27991)
|
||||
Outpt time (%) = 0.00594518 (0.0285638)
|
||||
Other time (%) = 17.6439 (84.7709)
|
||||
|
||||
Nlocal: 2171.25 ave 2428 max 1747 min
|
||||
Histogram: 1 0 0 0 1 1 2 1 0 2
|
||||
Nghost: 61.25 ave 69 max 54 min
|
||||
Histogram: 1 1 0 1 1 1 0 2 0 1
|
||||
Neighs: 175.625 ave 225 max 132 min
|
||||
Histogram: 1 1 1 1 1 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 1405
|
||||
Ave neighs/atom = 0.0808866
|
||||
Neighbor list builds = 5156
|
||||
Dangerous builds = 1
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
@ -1,237 +0,0 @@
|
||||
LAMMPS (1 Feb 2014)
|
||||
# SRD viscosity demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
200 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
200 settings made for mass
|
||||
group big type 1
|
||||
200 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 3.1029 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.4028231 0 0 0.83369167 -0.55065517
|
||||
100 9.5167872 2.392105 0 4.7237178 2.8319556
|
||||
200 13.564465 3.0352634 0 6.3585572 3.6388732
|
||||
300 13.133051 4.3835112 0 7.6011086 4.060051
|
||||
400 14.584346 5.5141254 0 9.0872901 4.4231056
|
||||
500 15.331515 6.6554832 0 10.411704 4.847642
|
||||
600 16.953755 7.4794317 0 11.633102 5.2020696
|
||||
700 16.503256 8.8572339 0 12.900532 5.6694613
|
||||
800 17.006131 9.877343 0 14.043845 5.5483363
|
||||
900 17.305927 11.081594 0 15.321546 6.2908201
|
||||
1000 18.122491 12.126462 0 16.566472 5.7536055
|
||||
Loop time of 0.0603173 on 8 procs for 1000 steps with 200 atoms
|
||||
|
||||
Pair time (%) = 0.00182396 (3.02395)
|
||||
Neigh time (%) = 0.000557959 (0.92504)
|
||||
Comm time (%) = 0.0127766 (21.1823)
|
||||
Outpt time (%) = 0.000280827 (0.465583)
|
||||
Other time (%) = 0.0448779 (74.4031)
|
||||
|
||||
Nlocal: 25 ave 30 max 20 min
|
||||
Histogram: 1 0 1 1 0 0 3 1 0 1
|
||||
Nghost: 28.375 ave 36 max 22 min
|
||||
Histogram: 1 0 1 2 1 0 2 0 0 1
|
||||
Neighs: 33.125 ave 45 max 22 min
|
||||
Histogram: 1 0 2 1 0 1 1 0 1 1
|
||||
|
||||
Total # of neighbors = 265
|
||||
Ave neighs/atom = 1.325
|
||||
Neighbor list builds = 99
|
||||
Dangerous builds = 96
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 29929 atoms
|
||||
|
||||
set type 2 mass 0.1
|
||||
29929 settings made for mass
|
||||
group small type 2
|
||||
29929 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
Deleted 12759 atoms, new total = 17370
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.dimer.mp
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 50000
|
||||
SRD info:
|
||||
SRD/big particles = 17170 200
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 75 75 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
|
||||
SRD per actual grid cell = 5.5499
|
||||
SRD viscosity = 0.235551
|
||||
big/SRD mass density ratio = 0.142367
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.20347 7.72323
|
||||
ave/max big velocity = 2.64047 6.60911
|
||||
Memory usage per processor = 7.0395 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 6.9744766 0 0.30175295 21.011259 26.207244 2.7219331 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.906187 3319 0.25279446 20.53509 21.955199 9.3471734 14560 77 77 9 6051 40320 5625 3319 1.2073941 0 1062 0
|
||||
2000 1.6009081 3420 0.25060769 20.572601 21.765278 12.835365 13521 63 63 1 7515 40320 5625 3420 1.1621445 0 1062 0
|
||||
3000 1.8288965 3342 0.25195284 20.519576 21.882104 7.1720562 13550 62 62 1 8561 40320 5625 3342 1.1411375 0 1062 0
|
||||
4000 1.8940522 3383 0.25185767 20.462769 21.873838 7.3011842 13210 55 55 0 9536 40320 5625 3383 1.1541274 0 1062 0
|
||||
5000 1.7848964 3377 0.25063675 20.438054 21.767801 5.7235852 13258 60 60 1 10628 40320 5625 3377 1.1401366 0 1062 0
|
||||
6000 2.0436442 3393 0.2528503 20.437534 21.960048 4.3266887 13369 65 65 1 11693 40320 5625 3393 1.1363335 0 1062 0
|
||||
7000 2.0248598 3377 0.25304247 20.468218 21.976738 9.1535003 13126 69 69 2 12819 40320 5625 3377 1.1556137 0 1062 0
|
||||
8000 1.9627172 3397 0.25201977 20.425693 21.887917 7.9563872 13216 58 58 3 14113 40320 5625 3397 1.144738 0 1062 0
|
||||
9000 2.4805409 3385 0.25688024 20.462046 22.310049 6.0178529 13031 42 42 1 15329 40320 5625 3385 1.1667813 0 1062 0
|
||||
10000 2.534712 3377 0.25802283 20.520922 22.409283 5.8494568 12804 49 50 1 16835 40320 5625 3377 1.1559636 0 1062 0
|
||||
11000 2.4295377 3368 0.25671703 20.485869 22.295874 7.0797587 13097 56 56 2 18180 40320 5625 3368 1.1634145 0 1062 0
|
||||
12000 2.5699389 3377 0.25784825 20.479516 22.39412 10.440503 13263 63 63 5 19848 40320 5625 3377 1.1714081 0 1062 0
|
||||
13000 2.5416625 3359 0.25893582 20.595038 22.488576 6.823793 12926 57 57 1 21307 40320 5625 3359 1.1478982 0 1062 0
|
||||
14000 2.9400702 3353 0.26140738 20.512878 22.703231 10.592709 12848 67 67 0 22782 40320 5625 3353 1.1642018 0 1062 0
|
||||
15000 2.7315042 3364 0.26050572 20.589951 22.624922 7.6633608 12640 49 49 0 24273 40320 5625 3364 1.1532394 0 1062 0
|
||||
16000 2.7176527 3389 0.25840703 20.418 22.442651 8.0150175 13019 59 59 1 25970 40320 5625 3389 1.1555937 0 1062 0
|
||||
17000 2.883266 3355 0.26040537 20.468173 22.616206 6.053208 12916 54 54 1 27532 40320 5625 3355 1.1363169 0 1062 0
|
||||
18000 2.8072496 3369 0.26013039 20.500924 22.592325 5.7179969 12989 45 45 0 29011 40320 5625 3369 1.1341799 0 1062 0
|
||||
19000 2.8007066 3372 0.2602809 20.51887 22.605396 8.9063895 12817 59 59 1 30504 40320 5625 3372 1.1253001 0 1062 0
|
||||
20000 3.0147455 3352 0.26233709 20.537991 22.783977 10.01786 13099 63 63 2 32100 40320 5625 3352 1.1263738 0 1062 0
|
||||
21000 2.5502874 3354 0.25762968 20.475174 22.375138 7.4525361 12917 55 55 3 33904 40320 5625 3354 1.1432482 0 1062 0
|
||||
22000 2.5643661 3357 0.25754499 20.45733 22.367782 9.5567227 12893 58 58 0 35500 40320 5625 3357 1.1309581 0 1062 0
|
||||
23000 2.8451307 3387 0.26090715 20.540164 22.659786 7.8308779 12735 65 65 2 37080 40320 5625 3387 1.1666359 0 1062 0
|
||||
24000 2.6241046 3341 0.25916876 20.553849 22.508807 9.7905794 12815 54 54 1 38864 40320 5625 3341 1.1422596 0 1062 0
|
||||
25000 2.6054468 3374 0.25897446 20.550874 22.491932 9.4099539 13094 59 59 4 40505 40320 5625 3374 1.1887482 0 1062 0
|
||||
26000 3.1370949 3356 0.26301193 20.50545 22.842586 9.930938 12785 59 59 0 42126 40320 5625 3356 1.1539158 0 1062 0
|
||||
27000 2.757373 3361 0.26029623 20.552484 22.606727 7.4336931 12687 59 59 2 43728 40320 5625 3361 1.1408006 0 1062 0
|
||||
28000 2.9939441 3393 0.26250984 20.568491 22.79898 9.201853 12802 66 66 0 45174 40320 5625 3393 1.1429688 0 1062 0
|
||||
29000 3.1611971 3376 0.26252235 20.444974 22.800066 8.2146139 13042 48 48 0 46696 40320 5625 3376 1.1370708 0 1062 0
|
||||
30000 2.2624796 3374 0.25475303 20.439753 22.125301 9.3304907 13249 53 53 1 48164 40320 5625 3374 1.1062325 0 1062 0
|
||||
31000 2.6864602 3393 0.2607928 20.648442 22.649855 7.6108593 13028 58 58 0 49556 40320 5625 3393 1.1154125 0 1062 0
|
||||
32000 2.8404087 3377 0.26037369 20.497351 22.613455 6.9017135 13055 63 63 1 51004 40320 5625 3377 1.1320087 0 1062 0
|
||||
33000 2.8467378 3365 0.26095982 20.543541 22.664361 7.194747 13306 58 58 0 52481 40320 5625 3365 1.1312548 0 1062 0
|
||||
34000 3.0833296 3382 0.26259198 20.509033 22.806114 7.44833 12988 59 60 1 54049 40320 5625 3382 1.1447344 0 1062 0
|
||||
35000 3.1068536 3382 0.26441995 20.650266 22.964872 9.3804156 13139 54 54 0 55749 40320 5625 3382 1.1272861 0 1062 0
|
||||
36000 2.6998442 3369 0.25864735 20.452138 22.463522 6.3327985 13317 52 52 0 57348 40320 5625 3369 1.1312386 0 1062 0
|
||||
37000 2.600171 3376 0.25882039 20.541424 22.478551 9.3909788 12841 57 57 0 58880 40320 5625 3376 1.1319429 0 1062 0
|
||||
38000 2.3962821 3367 0.25728672 20.560122 22.345352 7.4364329 13039 66 66 0 60627 40320 5625 3367 1.1468141 0 1062 0
|
||||
39000 2.8548804 3422 0.26044489 20.492753 22.619638 6.0832552 13249 50 50 0 62327 40320 5625 3422 1.1442726 0 1062 0
|
||||
40000 2.7721124 3375 0.25927374 20.452701 22.517924 10.368128 13197 55 55 1 63903 40320 5625 3375 1.140807 0 1062 0
|
||||
41000 3.0463159 3378 0.26123216 20.418508 22.688013 10.179554 13030 64 64 0 65629 40320 5625 3378 1.1277894 0 1062 0
|
||||
42000 2.9625288 3388 0.26205988 20.552817 22.759901 8.8326646 12958 64 64 0 67242 40320 5625 3388 1.159201 0 1062 0
|
||||
43000 2.7524867 3347 0.2592403 20.464417 22.51502 10.30221 12815 65 65 2 68734 40320 5625 3347 1.1444123 0 1062 0
|
||||
44000 2.8779981 3354 0.26009923 20.44551 22.589618 12.127509 12743 67 67 3 70309 40320 5625 3354 1.1467915 0 1062 0
|
||||
45000 2.7833999 3365 0.25968205 20.479753 22.553386 8.6942365 12909 46 47 0 71846 40320 5625 3365 1.1480348 0 1062 0
|
||||
46000 2.6564678 3370 0.25935897 20.546258 22.525327 9.2618375 12923 61 61 1 73491 40320 5625 3370 1.1528284 0 1062 0
|
||||
47000 2.821625 3414 0.25999655 20.47859 22.5807 7.5359036 12861 55 55 2 75201 40320 5625 3414 1.1395745 0 1062 0
|
||||
48000 2.9301623 3351 0.26139433 20.519127 22.702098 9.5177842 13037 49 49 2 76819 40320 5625 3351 1.1472505 0 1062 0
|
||||
49000 2.528824 3390 0.25834586 20.553364 22.437338 8.953785 13127 49 49 0 78450 40320 5625 3390 1.1495903 0 1062 0
|
||||
50000 3.0054471 3375 0.261046 20.432787 22.671845 7.9749959 13089 56 56 2 80717 40320 5625 3375 1.1574724 0 1062 0
|
||||
Loop time of 10.5055 on 8 procs for 50000 steps with 17370 atoms
|
||||
|
||||
Pair time (%) = 0.156617 (1.49081)
|
||||
Neigh time (%) = 0.556925 (5.30126)
|
||||
Comm time (%) = 0.902042 (8.58637)
|
||||
Outpt time (%) = 0.00305247 (0.0290559)
|
||||
Other time (%) = 8.88688 (84.5925)
|
||||
|
||||
Nlocal: 2171.25 ave 2567 max 1849 min
|
||||
Histogram: 2 0 0 1 1 2 1 0 0 1
|
||||
Nghost: 62.625 ave 71 max 57 min
|
||||
Histogram: 2 0 1 0 2 2 0 0 0 1
|
||||
Neighs: 168.25 ave 232 max 120 min
|
||||
Histogram: 1 0 1 2 2 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1346
|
||||
Ave neighs/atom = 0.0774899
|
||||
Neighbor list builds = 2599
|
||||
Dangerous builds = 17
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
312
examples/ASPHERE/dimer/log.1Feb24.dimer.g++.1
Normal file
312
examples/ASPHERE/dimer/log.1Feb24.dimer.g++.1
Normal file
@ -0,0 +1,312 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD diffusion demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
Reading data file ...
|
||||
orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
200 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
200 settings made for mass
|
||||
group big type 1
|
||||
200 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42
|
||||
ghost atom cutoff = 1.42
|
||||
binsize = 0.71, bins = 27 27 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.557 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.4028231 0 0 0.83369167 -0.55065517
|
||||
100 9.5167872 2.392105 0 4.7237178 2.8319556
|
||||
200 13.564465 3.0352634 0 6.3585572 3.6388732
|
||||
300 13.133051 4.3835112 0 7.6011086 4.060051
|
||||
400 14.576837 5.5141059 0 9.0854309 4.422762
|
||||
500 15.227825 6.6472106 0 10.378028 4.8598912
|
||||
600 16.93219 7.454865 0 11.603251 5.2908894
|
||||
700 16.573769 8.7323442 0 12.792918 5.3544684
|
||||
800 17.482599 9.7221047 0 14.005341 5.6200973
|
||||
900 18.548144 10.739353 0 15.283649 4.7817995
|
||||
1000 18.068079 12.058417 0 16.485096 6.5773091
|
||||
Loop time of 0.0511113 on 1 procs for 1000 steps with 200 atoms
|
||||
|
||||
Performance: 8452141.519 tau/day, 19565.142 timesteps/s, 3.913 Matom-step/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 | 0.0095507 | 0.0095507 | 0.0095507 | 0.0 | 18.69
|
||||
Neigh | 0.0042239 | 0.0042239 | 0.0042239 | 0.0 | 8.26
|
||||
Comm | 0.002203 | 0.002203 | 0.002203 | 0.0 | 4.31
|
||||
Output | 8.8531e-05 | 8.8531e-05 | 8.8531e-05 | 0.0 | 0.17
|
||||
Modify | 0.03336 | 0.03336 | 0.03336 | 0.0 | 65.27
|
||||
Other | | 0.001685 | | | 3.30
|
||||
|
||||
Nlocal: 200 ave 200 max 200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 64 ave 64 max 64 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 275 ave 275 max 275 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 275
|
||||
Ave neighs/atom = 1.375
|
||||
Neighbor list builds = 193
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
|
||||
create_atoms 2 region plane
|
||||
Created 29929 atoms
|
||||
using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
|
||||
create_atoms CPU = 0.007 seconds
|
||||
|
||||
set type 2 mass 0.1
|
||||
Setting atom values ...
|
||||
29929 settings made for mass
|
||||
group small type 2
|
||||
29929 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 14 14 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 12776 atoms, new total = 17353
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.dimer
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 17153 200
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 75 75 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
|
||||
SRD per actual grid cell = 5.544404
|
||||
SRD viscosity = 0.23553122
|
||||
big/SRD mass density ratio = 0.14250828
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.191188 7.6900178
|
||||
ave/max big velocity = 2.6813242 7.1846104
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 18.683304, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 26.77 | 26.77 | 26.77 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 6.8392143 0 0.297476 20.71529 25.810505 4.0555741 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.2285566 3375 0.24673495 20.492683 21.407958 5.237464 13477 54 54 1 652 16900 5625 3375 1.1653557 0 15 0
|
||||
2000 1.3561011 3395 0.24763991 20.476182 21.486477 9.2878509 13435 67 67 0 1504 16900 5625 3395 1.1651182 0 15 0
|
||||
3000 1.2445369 3352 0.24713723 20.515681 21.442861 8.0289529 13186 62 63 2 2379 16900 5625 3352 1.1746721 0 15 0
|
||||
4000 1.1058201 3389 0.24596239 20.51709 21.340926 10.003266 13466 66 66 0 3264 16900 5625 3389 1.1671415 0 15 0
|
||||
5000 1.0584198 3407 0.24539623 20.503281 21.291804 9.1119405 13254 64 64 0 4189 16900 5625 3407 1.1687685 0 15 0
|
||||
6000 1.3335611 3360 0.24737788 20.470239 21.463742 8.6885126 13281 62 62 1 5031 16900 5625 3360 1.1568996 0 15 0
|
||||
7000 1.1384759 3401 0.24570869 20.47075 21.318914 9.1801119 13059 47 47 1 5878 16900 5625 3401 1.182474 0 15 0
|
||||
8000 1.2982334 3397 0.24667224 20.435333 21.402517 6.5904007 13405 56 56 0 6729 16900 5625 3397 1.169017 0 24 0
|
||||
9000 1.0456752 3381 0.24504517 20.482316 21.261344 10.497413 13205 81 81 2 7706 16900 5625 3381 1.1694675 0 24 0
|
||||
10000 1.2222547 3394 0.24653264 20.479825 21.390405 8.7495888 13296 68 68 1 8581 16900 5625 3394 1.1613437 0 24 0
|
||||
Loop time of 7.18514 on 1 procs for 10000 steps with 17353 atoms
|
||||
|
||||
Performance: 120248.165 tau/day, 1391.761 timesteps/s, 24.151 Matom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14497 | 0.14497 | 0.14497 | 0.0 | 2.02
|
||||
Neigh | 0.031835 | 0.031835 | 0.031835 | 0.0 | 0.44
|
||||
Comm | 0.094201 | 0.094201 | 0.094201 | 0.0 | 1.31
|
||||
Output | 0.00082765 | 0.00082765 | 0.00082765 | 0.0 | 0.01
|
||||
Modify | 6.8507 | 6.8507 | 6.8507 | 0.0 | 95.35
|
||||
Other | | 0.06259 | | | 0.87
|
||||
|
||||
Nlocal: 17353 ave 17353 max 17353 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1334 ave 1334 max 1334 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1334
|
||||
Ave neighs/atom = 0.076874316
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
312
examples/ASPHERE/dimer/log.1Feb24.dimer.g++.4
Normal file
312
examples/ASPHERE/dimer/log.1Feb24.dimer.g++.4
Normal file
@ -0,0 +1,312 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD diffusion demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
Reading data file ...
|
||||
orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
200 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
200 settings made for mass
|
||||
group big type 1
|
||||
200 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42
|
||||
ghost atom cutoff = 1.42
|
||||
binsize = 0.71, bins = 27 27 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.553 | 5.553 | 5.553 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.4028231 0 0 0.83369167 -0.55065517
|
||||
100 9.5167872 2.392105 0 4.7237178 2.8319556
|
||||
200 13.564465 3.0352634 0 6.3585572 3.6388732
|
||||
300 13.133051 4.3835112 0 7.6011086 4.060051
|
||||
400 14.576837 5.5141059 0 9.0854309 4.422762
|
||||
500 15.227825 6.6472106 0 10.378028 4.8598912
|
||||
600 16.93219 7.454865 0 11.603251 5.2908894
|
||||
700 16.573769 8.7323442 0 12.792918 5.3544684
|
||||
800 17.482599 9.7221047 0 14.005341 5.6200973
|
||||
900 18.548144 10.739353 0 15.283649 4.7817995
|
||||
1000 18.068079 12.058417 0 16.485096 6.5773093
|
||||
Loop time of 0.0424792 on 4 procs for 1000 steps with 200 atoms
|
||||
|
||||
Performance: 10169676.521 tau/day, 23540.918 timesteps/s, 4.708 Matom-step/s
|
||||
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0022758 | 0.0023448 | 0.002442 | 0.1 | 5.52
|
||||
Neigh | 0.0011082 | 0.0011236 | 0.0011582 | 0.1 | 2.64
|
||||
Comm | 0.0099484 | 0.010092 | 0.010247 | 0.1 | 23.76
|
||||
Output | 9.551e-05 | 0.00010604 | 0.00013381 | 0.0 | 0.25
|
||||
Modify | 0.026025 | 0.026222 | 0.026405 | 0.1 | 61.73
|
||||
Other | | 0.00259 | | | 6.10
|
||||
|
||||
Nlocal: 50 ave 55 max 47 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 33.75 ave 38 max 32 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 68.75 ave 77 max 64 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 275
|
||||
Ave neighs/atom = 1.375
|
||||
Neighbor list builds = 193
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
|
||||
create_atoms 2 region plane
|
||||
Created 29929 atoms
|
||||
using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
set type 2 mass 0.1
|
||||
Setting atom values ...
|
||||
29929 settings made for mass
|
||||
group small type 2
|
||||
29929 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 14 14 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 12776 atoms, new total = 17353
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.dimer
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 17153 200
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 75 75 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
|
||||
SRD per actual grid cell = 5.544404
|
||||
SRD viscosity = 0.23553122
|
||||
big/SRD mass density ratio = 0.14250828
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.191188 7.6900178
|
||||
ave/max big velocity = 2.6813242 7.1846103
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 18.683304, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.2 | 13.21 | 13.22 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 6.8392143 0 0.297476 20.71529 25.810505 4.0555746 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.1648085 3389 0.24643931 20.514525 21.382307 5.5927686 13390 59 59 0 1015 28224 5625 3389 1.1513276 0 111 0
|
||||
2000 1.1870311 3385 0.24701637 20.548037 21.432375 5.9269821 13271 57 57 2 1878 28224 5625 3385 1.1619099 0 111 0
|
||||
3000 1.1362839 3365 0.24577276 20.477942 21.324474 5.1621045 13244 59 60 1 2778 28224 5625 3365 1.1807679 0 111 0
|
||||
4000 1.3023748 3390 0.24679509 20.442907 21.413176 5.6127077 13413 65 65 1 3705 28224 5625 3390 1.1726946 0 111 0
|
||||
5000 1.195496 3387 0.2458055 20.43667 21.327314 6.1843476 13248 51 51 1 4638 28224 5625 3387 1.1730279 0 111 0
|
||||
6000 1.2389419 3387 0.24546635 20.374876 21.297888 5.5909826 13184 54 54 1 5494 28224 5625 3387 1.1859134 0 111 0
|
||||
7000 1.2068912 3378 0.24564722 20.414447 21.313581 8.5604547 13188 57 57 1 6428 28224 5625 3378 1.1499181 0 111 0
|
||||
8000 1.1014154 3374 0.24514746 20.449665 21.270219 7.3483529 13179 63 63 0 7591 28224 5625 3374 1.1769322 0 121 0
|
||||
9000 1.356464 3388 0.24749513 20.463349 21.473915 7.6809833 13138 50 50 2 8485 28224 5625 3388 1.1448659 0 121 0
|
||||
10000 1.1632951 3402 0.24560819 20.44354 21.310195 9.5738599 13323 64 67 0 9304 28224 5625 3402 1.1550136 0 121 0
|
||||
Loop time of 2.47185 on 4 procs for 10000 steps with 17353 atoms
|
||||
|
||||
Performance: 349536.432 tau/day, 4045.561 timesteps/s, 70.203 Matom-step/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 | 0.037524 | 0.039903 | 0.042215 | 1.1 | 1.61
|
||||
Neigh | 0.01053 | 0.010805 | 0.011068 | 0.2 | 0.44
|
||||
Comm | 0.14536 | 0.14822 | 0.15102 | 0.6 | 6.00
|
||||
Output | 0.00051847 | 0.00054674 | 0.0006272 | 0.0 | 0.02
|
||||
Modify | 2.2276 | 2.2334 | 2.2381 | 0.3 | 90.35
|
||||
Other | | 0.03895 | | | 1.58
|
||||
|
||||
Nlocal: 4338.25 ave 4488 max 4277 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
Nghost: 76.75 ave 85 max 69 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 331.25 ave 355 max 306 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1325
|
||||
Ave neighs/atom = 0.076355673
|
||||
Neighbor list builds = 507
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
328
examples/ASPHERE/dimer/log.1Feb24.dimer.mp.g++.1
Normal file
328
examples/ASPHERE/dimer/log.1Feb24.dimer.mp.g++.1
Normal file
@ -0,0 +1,328 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD viscosity demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
Reading data file ...
|
||||
orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
200 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
200 settings made for mass
|
||||
group big type 1
|
||||
200 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42
|
||||
ghost atom cutoff = 1.42
|
||||
binsize = 0.71, bins = 27 27 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.557 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.4028231 0 0 0.83369167 -0.55065517
|
||||
100 9.5167872 2.392105 0 4.7237178 2.8319556
|
||||
200 13.564465 3.0352634 0 6.3585572 3.6388732
|
||||
300 13.133051 4.3835112 0 7.6011086 4.060051
|
||||
400 14.576837 5.5141059 0 9.0854309 4.422762
|
||||
500 15.227825 6.6472106 0 10.378028 4.8598912
|
||||
600 16.93219 7.454865 0 11.603251 5.2908894
|
||||
700 16.573769 8.7323442 0 12.792918 5.3544684
|
||||
800 17.482599 9.7221047 0 14.005341 5.6200973
|
||||
900 18.548144 10.739353 0 15.283649 4.7817995
|
||||
1000 18.068079 12.058417 0 16.485096 6.5773091
|
||||
Loop time of 0.0502552 on 1 procs for 1000 steps with 200 atoms
|
||||
|
||||
Performance: 8596132.389 tau/day, 19898.455 timesteps/s, 3.980 Matom-step/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 | 0.0095071 | 0.0095071 | 0.0095071 | 0.0 | 18.92
|
||||
Neigh | 0.0042809 | 0.0042809 | 0.0042809 | 0.0 | 8.52
|
||||
Comm | 0.0022049 | 0.0022049 | 0.0022049 | 0.0 | 4.39
|
||||
Output | 0.0001259 | 0.0001259 | 0.0001259 | 0.0 | 0.25
|
||||
Modify | 0.032467 | 0.032467 | 0.032467 | 0.0 | 64.60
|
||||
Other | | 0.00167 | | | 3.32
|
||||
|
||||
Nlocal: 200 ave 200 max 200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 64 ave 64 max 64 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 275 ave 275 max 275 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 275
|
||||
Ave neighs/atom = 1.375
|
||||
Neighbor list builds = 193
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
|
||||
create_atoms 2 region plane
|
||||
Created 29929 atoms
|
||||
using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
|
||||
create_atoms CPU = 0.006 seconds
|
||||
|
||||
set type 2 mass 0.1
|
||||
Setting atom values ...
|
||||
29929 settings made for mass
|
||||
group small type 2
|
||||
29929 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 14 14 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 12776 atoms, new total = 17353
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.dimer.mp
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 25000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 17153 200
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 75 75 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
|
||||
SRD per actual grid cell = 5.544404
|
||||
SRD viscosity = 0.23553122
|
||||
big/SRD mass density ratio = 0.14250828
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.191188 7.6900178
|
||||
ave/max big velocity = 2.6813242 7.1846104
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 18.683304, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 26.77 | 26.77 | 26.77 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 6.8392143 0 0.297476 20.71529 25.810505 4.0555741 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.3421139 3394 0.24797209 20.515424 21.515299 5.9986227 13474 52 52 1 704 16900 5625 3394 1.1328453 0 14 0
|
||||
2000 1.3372296 3366 0.24694513 20.429958 21.426194 9.640193 13302 74 74 0 1516 16900 5625 3366 1.1634167 0 14 0
|
||||
3000 1.4022742 3360 0.24799552 20.472637 21.517331 5.9446731 13483 47 47 0 2989 16900 5625 3360 1.1774442 0 217 0
|
||||
4000 1.6325677 3376 0.25066282 20.532497 21.74876 6.9698781 13206 61 61 2 4198 16900 5625 3376 1.1749717 0 217 0
|
||||
5000 2.0992887 3391 0.25484065 20.547279 22.111249 10.648531 13414 62 69 1 6389 16900 5625 3391 1.1862903 0 412 0
|
||||
6000 1.7584548 3388 0.25126127 20.490636 21.800684 8.68036 13456 58 58 0 7672 16900 5625 3388 1.1553986 0 412 0
|
||||
7000 2.2384486 3343 0.25650382 20.58791 22.255554 12.008146 13187 59 59 0 8879 16900 5625 3343 1.1728994 0 412 0
|
||||
8000 2.4981644 3380 0.25734806 20.467672 22.328804 6.7156077 13383 51 51 0 10085 16900 5625 3380 1.156205 0 412 0
|
||||
9000 2.4321991 3384 0.25838085 20.606426 22.418415 9.9820399 12847 55 55 0 11445 16900 5625 3384 1.156145 0 412 0
|
||||
10000 2.2560205 3387 0.25541566 20.480404 22.161139 10.87418 13022 66 66 0 12863 16900 5625 3387 1.1559136 0 412 0
|
||||
11000 2.2321955 3378 0.25533735 20.491359 22.154345 8.510825 13175 70 70 1 14273 16900 5625 3378 1.1470284 0 412 0
|
||||
12000 2.2715125 3377 0.25469529 20.40636 22.098637 9.0604601 13146 68 68 0 15742 16900 5625 3377 1.171755 0 412 0
|
||||
13000 2.3766974 3364 0.25667348 20.499635 22.270275 10.766786 12829 60 60 1 17214 16900 5625 3364 1.130354 0 412 0
|
||||
14000 2.5659704 3347 0.25802994 20.47632 22.387967 8.2568074 13090 66 66 1 18767 16900 5625 3347 1.1609852 0 412 0
|
||||
15000 2.3235671 3400 0.25603152 20.483517 22.214574 5.4785711 13389 50 50 0 20173 16900 5625 3400 1.149754 0 412 0
|
||||
16000 2.6335413 3373 0.25956137 20.558854 22.520843 4.7121947 13027 58 58 1 21668 16900 5625 3373 1.1308267 0 412 0
|
||||
17000 2.5603168 3410 0.25744829 20.430065 22.337501 6.1898616 13218 51 51 1 23170 16900 5625 3410 1.1285699 0 412 0
|
||||
18000 2.7801428 3362 0.26002524 20.489884 22.56109 8.9919312 13002 57 57 3 24829 16900 5625 3362 1.1610153 0 412 0
|
||||
19000 2.7869738 3364 0.26033026 20.51126 22.587555 9.6539159 13085 46 46 0 26476 16900 5625 3364 1.1431913 0 412 0
|
||||
20000 2.678182 3383 0.2586317 20.444934 22.44018 7.3468277 12939 42 42 0 27992 16900 5625 3383 1.143534 0 412 0
|
||||
21000 2.8094503 3375 0.26088069 20.542272 22.635313 8.2257869 13449 52 52 0 29570 16900 5625 3375 1.1375499 0 412 0
|
||||
22000 3.2220363 3377 0.26464914 20.561866 22.962283 6.6329375 13178 65 65 6 31203 16900 5625 3377 1.1683184 0 412 0
|
||||
23000 3.2268368 3339 0.26414495 20.514543 22.918536 4.6879815 12589 51 51 0 32929 16900 5625 3339 1.1378613 0 412 0
|
||||
24000 2.6062461 3380 0.25967238 20.588821 22.530474 10.036449 12745 53 54 0 34460 16900 5625 3380 1.1396017 0 412 0
|
||||
25000 3.2519674 3373 0.26376614 20.462953 22.885669 7.7592712 12856 52 52 1 36172 16900 5625 3373 1.1858891 0 412 0
|
||||
Loop time of 20.7208 on 1 procs for 25000 steps with 17353 atoms
|
||||
|
||||
Performance: 104243.242 tau/day, 1206.519 timesteps/s, 20.937 Matom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.39343 | 0.39343 | 0.39343 | 0.0 | 1.90
|
||||
Neigh | 0.09039 | 0.09039 | 0.09039 | 0.0 | 0.44
|
||||
Comm | 0.26483 | 0.26483 | 0.26483 | 0.0 | 1.28
|
||||
Output | 0.0021023 | 0.0021023 | 0.0021023 | 0.0 | 0.01
|
||||
Modify | 19.785 | 19.785 | 19.785 | 0.0 | 95.49
|
||||
Other | | 0.1847 | | | 0.89
|
||||
|
||||
Nlocal: 17353 ave 17353 max 17353 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 146 ave 146 max 146 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1326 ave 1326 max 1326 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1326
|
||||
Ave neighs/atom = 0.0764133
|
||||
Neighbor list builds = 1290
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:21
|
||||
328
examples/ASPHERE/dimer/log.1Feb24.dimer.mp.g++.4
Normal file
328
examples/ASPHERE/dimer/log.1Feb24.dimer.mp.g++.4
Normal file
@ -0,0 +1,328 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD viscosity demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
Reading data file ...
|
||||
orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
200 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
200 settings made for mass
|
||||
group big type 1
|
||||
200 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42
|
||||
ghost atom cutoff = 1.42
|
||||
binsize = 0.71, bins = 27 27 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.553 | 5.553 | 5.553 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.4028231 0 0 0.83369167 -0.55065517
|
||||
100 9.5167872 2.392105 0 4.7237178 2.8319556
|
||||
200 13.564465 3.0352634 0 6.3585572 3.6388732
|
||||
300 13.133051 4.3835112 0 7.6011086 4.060051
|
||||
400 14.576837 5.5141059 0 9.0854309 4.422762
|
||||
500 15.227825 6.6472106 0 10.378028 4.8598912
|
||||
600 16.93219 7.454865 0 11.603251 5.2908894
|
||||
700 16.573769 8.7323442 0 12.792918 5.3544684
|
||||
800 17.482599 9.7221047 0 14.005341 5.6200973
|
||||
900 18.548144 10.739353 0 15.283649 4.7817995
|
||||
1000 18.068079 12.058417 0 16.485096 6.5773093
|
||||
Loop time of 0.0421376 on 4 procs for 1000 steps with 200 atoms
|
||||
|
||||
Performance: 10252121.014 tau/day, 23731.762 timesteps/s, 4.746 Matom-step/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 | 0.002222 | 0.0023177 | 0.0024199 | 0.2 | 5.50
|
||||
Neigh | 0.0010943 | 0.0011428 | 0.001174 | 0.1 | 2.71
|
||||
Comm | 0.0097533 | 0.009878 | 0.010001 | 0.1 | 23.44
|
||||
Output | 9.4323e-05 | 0.0001028 | 0.00012783 | 0.0 | 0.24
|
||||
Modify | 0.02557 | 0.026225 | 0.026638 | 0.3 | 62.24
|
||||
Other | | 0.002471 | | | 5.86
|
||||
|
||||
Nlocal: 50 ave 55 max 47 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 33.75 ave 38 max 32 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 68.75 ave 77 max 64 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 275
|
||||
Ave neighs/atom = 1.375
|
||||
Neighbor list builds = 193
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
|
||||
create_atoms 2 region plane
|
||||
Created 29929 atoms
|
||||
using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
set type 2 mass 0.1
|
||||
Setting atom values ...
|
||||
29929 settings made for mass
|
||||
group small type 2
|
||||
29929 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 14 14 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 12776 atoms, new total = 17353
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.dimer.mp
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 25000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 17153 200
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 75 75 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
|
||||
SRD per actual grid cell = 5.544404
|
||||
SRD viscosity = 0.23553122
|
||||
big/SRD mass density ratio = 0.14250828
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.191188 7.6900178
|
||||
ave/max big velocity = 2.6813242 7.1846103
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 18.683304, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.2 | 13.21 | 13.22 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 6.8392143 0 0.297476 20.71529 25.810505 4.0555746 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.2739082 3360 0.24704957 20.486195 21.435256 3.6693454 13497 46 46 2 816 28224 5625 3360 1.1564821 0 54 0
|
||||
2000 1.3843858 3380 0.24759985 20.451634 21.483001 5.2299666 13363 70 70 0 1671 28224 5625 3380 1.170199 0 54 0
|
||||
3000 1.3942166 3373 0.24823326 20.499268 21.537959 7.7943821 13214 59 59 2 2600 28224 5625 3373 1.1539593 0 54 0
|
||||
4000 1.6387342 3366 0.24966206 20.441071 21.661928 4.3859226 13280 49 49 2 3568 28224 5625 3366 1.176006 0 54 0
|
||||
5000 1.8677297 3388 0.25278915 20.541792 21.933251 5.9053775 13238 68 68 2 4553 28224 5625 3388 1.1728833 0 54 0
|
||||
6000 1.8884914 3372 0.25216944 20.472555 21.879481 7.5864922 13142 62 62 1 5645 28224 5625 3372 1.1733967 0 54 0
|
||||
7000 2.0575519 3387 0.25374609 20.483403 22.016279 6.9842803 13101 41 41 0 6805 28224 5625 3387 1.1503024 0 54 0
|
||||
8000 1.9800593 3373 0.252975 20.474232 21.949376 8.3493951 13176 63 64 1 8166 28224 5625 3373 1.1621339 0 67 0
|
||||
9000 2.2288114 3403 0.25526729 20.487802 22.148267 6.7676677 12866 61 61 1 9360 28224 5625 3403 1.1446891 0 67 0
|
||||
10000 2.4854456 3339 0.25713924 20.45903 22.310687 9.3781009 12692 65 65 1 10680 28224 5625 3339 1.1417733 0 67 0
|
||||
11000 2.5850677 3335 0.25820147 20.476975 22.402851 9.9421534 12954 70 70 2 11964 28224 5625 3335 1.1497985 0 67 0
|
||||
12000 2.5087529 3358 0.25746572 20.469992 22.339013 9.9566718 12959 58 58 0 13462 28224 5625 3358 1.1365643 0 98 0
|
||||
13000 2.5480838 3371 0.25761214 20.453395 22.351717 8.6628089 13142 54 54 3 14985 28224 5625 3371 1.1510123 0 98 0
|
||||
14000 2.946645 3384 0.26176446 20.516743 22.711994 8.5668798 12579 53 53 0 16336 28224 5625 3384 1.1546089 0 98 0
|
||||
15000 4.025292 3338 0.27188564 20.591315 23.590157 9.8722859 12824 50 50 15 18115 28224 5625 3338 1.164518 0 122 0
|
||||
16000 2.2744945 3376 0.25598709 20.516221 22.21072 9.1890215 13020 52 52 0 19689 28224 5625 3376 1.1439385 0 122 0
|
||||
17000 2.3857021 3353 0.25662954 20.489114 22.266462 10.24809 12776 51 51 0 21158 28224 5625 3353 1.1435041 0 122 0
|
||||
18000 2.9678193 3330 0.26255063 20.56918 22.780206 8.6799225 12810 49 49 2 23066 28224 5625 3330 1.1567395 0 133 0
|
||||
19000 2.7464034 3368 0.2613984 20.634162 22.680232 9.5420188 12746 47 47 3 24675 28224 5625 3368 1.1426658 0 133 0
|
||||
20000 2.8228684 3367 0.26137363 20.575046 22.678083 8.0865322 12886 51 51 0 26119 28224 5625 3367 1.1484398 0 133 0
|
||||
21000 2.8903033 3389 0.26173565 20.556218 22.709494 11.038294 13152 41 41 1 27685 28224 5625 3389 1.1398936 0 133 0
|
||||
22000 2.8279828 3331 0.26058759 20.503035 22.609882 8.3647396 12895 57 57 1 29333 28224 5625 3331 1.1551348 0 133 0
|
||||
23000 2.9320035 3376 0.26178899 20.529779 22.714121 7.1841698 13077 54 54 1 30908 28224 5625 3376 1.1453809 0 133 0
|
||||
24000 2.8508425 3366 0.26104722 20.525884 22.649762 10.680819 13019 58 58 4 32831 28224 5625 3366 1.1391852 0 154 0
|
||||
25000 2.7878254 3333 0.25961 20.448132 22.525062 11.149479 12960 57 57 1 34494 28224 5625 3333 1.172964 0 154 0
|
||||
Loop time of 6.5335 on 4 procs for 25000 steps with 17353 atoms
|
||||
|
||||
Performance: 330603.792 tau/day, 3826.433 timesteps/s, 66.400 Matom-step/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 | 0.097519 | 0.10401 | 0.10744 | 1.2 | 1.59
|
||||
Neigh | 0.027038 | 0.028067 | 0.028678 | 0.4 | 0.43
|
||||
Comm | 0.39354 | 0.39697 | 0.40246 | 0.6 | 6.08
|
||||
Output | 0.0013442 | 0.0014045 | 0.0015827 | 0.3 | 0.02
|
||||
Modify | 5.8667 | 5.8905 | 5.9143 | 0.8 | 90.16
|
||||
Other | | 0.1126 | | | 1.72
|
||||
|
||||
Nlocal: 4338.25 ave 4476 max 4199 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 78.5 ave 83 max 75 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Neighs: 328 ave 352 max 309 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1312
|
||||
Ave neighs/atom = 0.075606523
|
||||
Neighbor list builds = 1274
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
@ -116,4 +116,4 @@ thermo 1000
|
||||
#dump 2 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
run 10000
|
||||
|
||||
@ -117,4 +117,4 @@ thermo 1000
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 50000
|
||||
run 10000
|
||||
|
||||
@ -1,190 +0,0 @@
|
||||
LAMMPS (1 Feb 2014)
|
||||
# SRD diffusion demo - ellipsoids
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big ellipsoidal particles
|
||||
|
||||
lattice sq 0.14
|
||||
Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
100 settings made for mass
|
||||
set type 1 shape 3.0 1.0 1.0
|
||||
100 settings made for shape
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big quat/random 29898
|
||||
100 settings made for quat/random
|
||||
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute rot big temp/asphere
|
||||
|
||||
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z # quatw quati quatj quatk
|
||||
|
||||
thermo_style custom step temp c_rot epair etotal press
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 3.31932 Mbytes
|
||||
Step Temp rot E_pair TotEng Press
|
||||
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
|
||||
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
|
||||
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
|
||||
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
|
||||
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
|
||||
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
|
||||
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
|
||||
700 2.9593679 2.8231211 -0.40051714 2.5292571 1.1630889
|
||||
800 2.7632971 2.9060854 -0.52075339 2.2149107 0.77106814
|
||||
900 2.9905601 2.8869672 -0.49099457 2.4696599 0.69616725
|
||||
1000 2.8470146 2.9004954 -0.51281252 2.305732 0.68820531
|
||||
Loop time of 0.0485955 on 8 procs for 1000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 0.0201517 (41.4682)
|
||||
Neigh time (%) = 0.000492364 (1.01319)
|
||||
Comm time (%) = 0.0191883 (39.4858)
|
||||
Outpt time (%) = 0.000273198 (0.562188)
|
||||
Other time (%) = 0.00848994 (17.4706)
|
||||
|
||||
Nlocal: 12.5 ave 16 max 8 min
|
||||
Histogram: 1 1 0 0 0 3 0 0 1 2
|
||||
Nghost: 34.125 ave 42 max 28 min
|
||||
Histogram: 1 0 2 2 0 1 0 1 0 1
|
||||
Neighs: 46.125 ave 65 max 20 min
|
||||
Histogram: 1 0 1 0 1 2 0 0 1 2
|
||||
|
||||
Total # of neighbors = 369
|
||||
Ave neighs/atom = 3.69
|
||||
Neighbor list builds = 174
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 120.0
|
||||
Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
|
||||
create_atoms 2 region plane
|
||||
Created 85849 atoms
|
||||
|
||||
set type 2 mass 0.01
|
||||
85849 settings made for mass
|
||||
group small type 2
|
||||
85849 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 2.0
|
||||
|
||||
neigh_modify one 10000
|
||||
|
||||
delete_atoms overlap 1.6 small big
|
||||
Deleted 71060 atoms, new total = 14889
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/asphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press 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[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all custom 1000 dump.ellipsoid id type x y z # quatw quati quatj quatk
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 14789 100
|
||||
big particle diameter max/min = 3 1
|
||||
SRD temperature & lamda = 1 0.1
|
||||
SRD max distance & max velocity = 0.4 40
|
||||
SRD grid counts: 107 107 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
|
||||
SRD per actual grid cell = 1.92757
|
||||
SRD viscosity = 0.688101
|
||||
big/SRD mass density ratio = 1.37367
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 13.3093 24.3359
|
||||
ave/max big velocity = 2.08028 5.05671
|
||||
Memory usage per processor = 10.9077 Mbytes
|
||||
Step Temp rot 2[9] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 2.9004954 2.9004954 0 0.025582146 -0.51281252 3.8089257 0.89865242 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 3.3106106 3.3106106 1.0635866 0.029956176 -0.47263474 4.4601751 1.8111247 14000 35 160 0 224946 98040 11449 4182 1.0635866 1047 50 0
|
||||
2000 2.2814487 2.2814487 1.2237286 0.017972589 -0.72341981 2.6759388 1.3454977 15318 47 276 0 528340 98040 11449 4136 1.2237286 2383 50 0
|
||||
3000 4.2476485 4.2476485 1.2992612 0.038526442 -0.59279435 5.7362019 1.6896403 16506 63 410 0 830594 98040 11449 4172 1.2992612 3834 50 0
|
||||
4000 2.4798681 2.4798681 1.3453264 0.022837826 -0.29467953 3.4003239 2.0765724 17201 51 403 0 1185573 98040 11449 4233 1.3453264 5456 50 0
|
||||
5000 3.0852629 3.0852629 1.3915904 0.02760985 -0.48621111 4.1108305 1.2676357 17540 61 591 0 1594856 98040 11449 4306 1.3915904 7419 50 0
|
||||
6000 6.7201122 6.7201122 1.3649223 0.064627842 -0.39052776 9.6224394 2.5524159 17997 59 564 0 2010250 98040 11449 4213 1.3649223 9280 50 0
|
||||
7000 2.720343 2.720343 1.3909677 0.024282471 -0.43789405 3.6154171 1.5288376 17922 64 342 0 2392388 98040 11449 4228 1.3909677 10947 50 0
|
||||
8000 1.9181626 1.9181626 1.3514483 0.014305579 -0.72810462 2.1299577 0.89423917 18188 42 260 0 2751626 98040 11449 4236 1.3514483 12556 50 0
|
||||
9000 2.9090186 2.9090186 1.3688847 0.02558926 -0.52445278 3.8099849 1.1756318 18536 63 440 0 3112508 98040 11449 4227 1.3688847 14164 50 0
|
||||
10000 1.9647403 1.9647403 1.3979066 0.015375037 -0.63827389 2.2891892 0.65597214 18817 60 466 0 3501352 98040 11449 4257 1.3979066 16016 50 0
|
||||
11000 1.9989051 1.9989051 1.3872043 0.016191243 -0.56765443 2.4107142 0.80582429 18756 58 767 0 3856028 98040 11449 4254 1.3872043 17611 50 0
|
||||
12000 1.7538755 1.7538755 1.4594883 0.013930543 -0.53915598 2.0741185 1.0563875 18602 58 335 0 4248666 98040 11449 4251 1.4594883 19350 50 0
|
||||
13000 13.730871 13.730871 1.4864545 0.13447802 -0.43656501 20.022433 3.6701166 19144 74 681 0 4708523 98040 11449 4104 1.4864545 21589 50 0
|
||||
14000 5.1078782 5.1078782 1.3637807 0.049721182 -0.20775172 7.4029868 2.559935 18494 65 713 0 5139143 98040 11449 4167 1.3637807 23555 50 0
|
||||
15000 2.5843962 2.5843962 1.3450247 0.022294373 -0.53134114 3.3194092 1.1069147 18489 52 260 0 5489252 98040 11449 4262 1.3450247 25209 50 0
|
||||
ERROR: Lost atoms: original 14889 current 14819 (../thermo.cpp:392)
|
||||
@ -1,247 +0,0 @@
|
||||
LAMMPS (1 Feb 2014)
|
||||
# SRD viscosity demo - ellipsoids
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big ellipsoidal particles
|
||||
|
||||
lattice sq 0.14
|
||||
Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
100 settings made for mass
|
||||
set type 1 shape 3.0 1.0 1.0
|
||||
100 settings made for shape
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big quat/random 29898
|
||||
100 settings made for quat/random
|
||||
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute rot big temp/asphere
|
||||
|
||||
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z # quatw quati quatj quatk
|
||||
|
||||
thermo_style custom step temp c_rot epair etotal press
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 3.31932 Mbytes
|
||||
Step Temp rot E_pair TotEng Press
|
||||
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
|
||||
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
|
||||
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
|
||||
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
|
||||
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
|
||||
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
|
||||
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
|
||||
700 2.9593679 2.8231211 -0.40051714 2.5292571 1.1630889
|
||||
800 2.7632971 2.9060854 -0.52075339 2.2149107 0.77106814
|
||||
900 2.9905601 2.8869672 -0.49099457 2.4696599 0.69616725
|
||||
1000 2.8470146 2.9004954 -0.51281252 2.305732 0.68820531
|
||||
Loop time of 0.0581853 on 8 procs for 1000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 0.0202803 (34.8546)
|
||||
Neigh time (%) = 0.000480682 (0.826122)
|
||||
Comm time (%) = 0.0264942 (45.5342)
|
||||
Outpt time (%) = 0.000326395 (0.560958)
|
||||
Other time (%) = 0.0106037 (18.2241)
|
||||
|
||||
Nlocal: 12.5 ave 16 max 8 min
|
||||
Histogram: 1 1 0 0 0 3 0 0 1 2
|
||||
Nghost: 34.125 ave 42 max 28 min
|
||||
Histogram: 1 0 2 2 0 1 0 1 0 1
|
||||
Neighs: 46.125 ave 65 max 20 min
|
||||
Histogram: 1 0 1 0 1 2 0 0 1 2
|
||||
|
||||
Total # of neighbors = 369
|
||||
Ave neighs/atom = 3.69
|
||||
Neighbor list builds = 174
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 120.0
|
||||
Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
|
||||
create_atoms 2 region plane
|
||||
Created 85849 atoms
|
||||
|
||||
set type 2 mass 0.01
|
||||
85849 settings made for mass
|
||||
group small type 2
|
||||
85849 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 2.0
|
||||
|
||||
neigh_modify one 10000
|
||||
|
||||
delete_atoms overlap 1.6 small big
|
||||
Deleted 71060 atoms, new total = 14889
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
|
||||
fix 3 small viscosity 20 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/asphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press 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[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all custom 500 dump.ellipsoid.mp id type x y z # quatw quati quatj quatk
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 50000
|
||||
SRD info:
|
||||
SRD/big particles = 14789 100
|
||||
big particle diameter max/min = 3 1
|
||||
SRD temperature & lamda = 1 0.1
|
||||
SRD max distance & max velocity = 0.4 40
|
||||
SRD grid counts: 107 107 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
|
||||
SRD per actual grid cell = 1.92757
|
||||
SRD viscosity = 0.688101
|
||||
big/SRD mass density ratio = 1.37367
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 13.3093 24.3359
|
||||
ave/max big velocity = 2.08028 5.05671
|
||||
Memory usage per processor = 10.9077 Mbytes
|
||||
Step Temp rot 2[9] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 2.9004954 2.9004954 0 0.025582146 -0.51281252 3.8089257 0.89865242 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 3.1663129 3.1663129 1.0612788 0.028825811 -0.42593131 4.291875 1.8917479 14347 45 319 0 247730 98040 11449 4128 1.0612788 1160 50 0
|
||||
2000 2.3854865 2.3854865 1.2711805 0.019550917 -0.6434388 2.910936 1.4342405 15199 41 151 0 526468 98040 11449 4191 1.2711805 2321 50 0
|
||||
3000 2.6796789 2.6796789 1.2494843 0.023573743 -0.48282696 3.5098946 1.6090734 16441 52 230 0 827117 98040 11449 4203 1.2494843 3659 50 0
|
||||
4000 2.7945661 2.7945661 1.3021617 0.024256529 -0.5523488 3.6115547 1.2702377 16935 52 474 0 1127934 98040 11449 4215 1.3021617 4966 50 0
|
||||
5000 2.7061959 2.7061959 1.338483 0.023736966 -0.498035 3.5341969 1.2801942 17578 49 277 0 1435089 98040 11449 4261 1.338483 6351 50 0
|
||||
6000 3.2698703 3.2698703 1.3285507 0.029840303 -0.42918398 4.4429227 1.4528039 17882 63 228 0 1776449 98040 11449 4252 1.3285507 7935 50 0
|
||||
7000 3.9340641 3.9340641 1.3823898 0.035368008 -0.59581277 5.2659427 1.1321242 18069 49 462 0 2090062 98040 11449 4265 1.3823898 9343 50 0
|
||||
8000 3.6037728 3.6037728 1.4150583 0.032400676 -0.54548483 4.8241367 1.2091317 18275 56 369 0 2486575 98040 11449 4229 1.4150583 11121 50 0
|
||||
9000 105.15275 105.15275 1.3630934 1.0504642 -0.27397996 156.40361 23.278069 18139 107 732 0 2861341 98040 11449 4217 1.3630934 12781 50 0
|
||||
10000 3.5224307 3.5224307 1.3897056 0.0324883 -0.4112387 4.837183 1.6093705 19100 61 347 0 3248400 98040 11449 4204 1.3897056 14424 50 0
|
||||
11000 4.1949959 4.1949959 1.421272 0.03853305 -0.51335814 5.7371858 1.3586332 18670 52 590 0 3722041 98040 11449 4263 1.421272 16373 50 0
|
||||
12000 3.1692742 3.1692742 1.3999982 0.028463927 -0.48422456 4.237994 1.1713046 18787 61 323 0 4117517 98040 11449 4202 1.3999982 18125 50 0
|
||||
13000 3.5868757 3.5868757 1.3193021 0.032298734 -0.53548629 4.8089585 1.0664078 18572 67 224 0 4417636 98040 11449 4277 1.3193021 19546 50 0
|
||||
14000 3.708681 3.708681 1.317797 0.033355183 -0.55968141 4.9662533 1.3959088 18284 67 207 0 4675359 98040 11449 4253 1.317797 20631 50 0
|
||||
15000 3.7410393 3.7410393 1.4017441 0.033377852 -0.60452027 4.9696283 1.2506767 18385 51 189 0 4956150 98040 11449 4275 1.4017441 21763 50 0
|
||||
16000 5.3298522 5.3298522 1.3456075 0.049673767 -0.54555257 7.3959272 1.841432 18693 63 549 0 5301393 98040 11449 4196 1.3456075 23216 50 0
|
||||
17000 3.7425275 3.7425275 1.321554 0.036608704 -0.12569607 5.4506699 2.3767421 18377 68 526 0 5637038 98040 11449 4261 1.321554 24829 50 0
|
||||
18000 6.1904009 6.1904009 1.3905006 0.05857936 -0.50181651 8.7218809 1.7936734 18422 63 522 0 6049781 98040 11449 4280 1.3905006 26646 50 0
|
||||
19000 3.1770374 3.1770374 1.3694174 0.028096405 -0.55051202 4.1832737 0.98036773 18342 54 343 0 6383253 98040 11449 4239 1.3694174 28038 50 0
|
||||
20000 3.5793112 3.5793112 1.3160294 0.031413769 -0.65597761 4.677196 1.0713128 18739 60 272 0 6692090 98040 11449 4262 1.3160294 29389 50 0
|
||||
21000 3.2300481 3.2300481 1.3407923 0.027955254 -0.65051393 4.1622578 0.89783071 18582 55 456 0 6999361 98040 11449 4237 1.3407923 30653 50 0
|
||||
22000 3.5879886 3.5879886 1.3790201 0.031692391 -0.6274228 4.7186802 0.97752405 18768 63 552 0 7350833 98040 11449 4308 1.3790201 32120 50 0
|
||||
23000 3.5666316 3.5666316 1.4123826 0.031275136 -0.6577261 4.656555 0.99950405 18864 49 231 0 7741276 98040 11449 4265 1.4123826 33939 50 0
|
||||
24000 3.7306353 3.7306353 1.3854831 0.032426295 -0.7306956 4.827951 0.93575015 18488 63 552 0 8096740 98040 11449 4238 1.3854831 35503 50 0
|
||||
25000 4.2971901 4.2971901 1.4207289 0.038358698 -0.69158669 5.7112265 1.0308127 18922 58 430 0 8518804 98040 11449 4254 1.4207289 37429 50 0
|
||||
26000 9.514164 9.514164 1.4209186 0.09200552 -0.47740255 13.698702 2.4102159 18934 63 570 0 8931705 98040 11449 4233 1.4209186 39132 50 0
|
||||
27000 3.9153535 3.9153535 1.3814961 0.036650525 -0.37698007 5.4568967 1.4531475 19153 65 553 0 9277922 98040 11449 4299 1.3814961 40660 50 0
|
||||
28000 3.6560048 3.6560048 1.3520603 0.033100525 -0.51910991 4.9283372 1.3474705 19529 59 447 0 9642607 98040 11449 4278 1.3520603 42335 50 0
|
||||
29000 14.835118 14.835118 1.3981622 0.14535835 -0.4619207 21.642405 3.6917556 19265 52 102 0 9937354 98040 11449 4224 1.3981622 43664 50 0
|
||||
30000 5.3595251 5.3595251 1.3636194 0.050893845 -0.40810785 7.5775845 1.7023989 19065 43 131 0 10261222 98040 11449 4170 1.3636194 45193 50 0
|
||||
31000 5.1821698 5.1821698 1.3180039 0.049074014 -0.41480304 7.30663 1.6943582 19142 58 282 0 10584027 98040 11449 4228 1.3180039 46636 50 0
|
||||
32000 4.3056534 4.3056534 1.3508467 0.040670309 -0.36002116 6.0554024 1.7875405 19065 36 284 0 10933981 98040 11449 4286 1.3508467 48240 50 0
|
||||
33000 3.8277999 3.8277999 1.3770405 0.034411971 -0.57982354 5.1235984 1.1046562 18838 71 729 0 11329901 98040 11449 4257 1.3770405 50046 50 0
|
||||
34000 4.6562056 4.6562056 1.3938501 0.043777831 -0.41966518 6.5180812 1.3815841 18914 61 269 0 11758952 98040 11449 4221 1.3938501 51773 50 0
|
||||
35000 3.4251492 3.4251492 1.3813031 0.031876928 -0.35731644 4.7461558 1.4152845 18838 60 283 0 12159425 98040 11449 4238 1.3813031 53477 50 0
|
||||
36000 4.2565688 4.2565688 1.3474871 0.039214915 -0.5035788 5.8387088 1.1222014 18765 56 240 0 12568711 98040 11449 4249 1.3474871 55170 50 0
|
||||
37000 5.3745505 5.3745505 1.4215553 0.053606226 -0.02664916 7.981431 2.8011643 19103 58 504 0 12941065 98040 11449 4270 1.4215553 56743 50 0
|
||||
38000 4.0346121 4.0346121 1.4354472 0.036753623 -0.53932498 5.472247 1.1475792 18829 62 623 0 13351480 98040 11449 4226 1.4354472 58443 50 0
|
||||
39000 4.0471971 4.0471971 1.417888 0.037884509 -0.3896991 5.6406246 1.3824278 19047 70 579 0 13752101 98040 11449 4219 1.417888 60208 50 0
|
||||
40000 4.1611575 4.1611575 1.3712048 0.039505792 -0.31810741 5.8820173 1.6615204 18811 65 378 0 14143802 98040 11449 4313 1.3712048 61793 50 0
|
||||
41000 4.852673 4.852673 1.3719985 0.044831688 -0.5554927 6.67499 1.2744313 18899 53 414 0 14505662 98040 11449 4274 1.3719985 63358 50 0
|
||||
42000 4.8338875 4.8338875 1.3595624 0.045465888 -0.43307636 6.7694161 1.6297026 18708 46 360 0 14839866 98040 11449 4224 1.3595624 64895 50 0
|
||||
43000 5.0243115 5.0243115 1.4371431 0.047111836 -0.47174292 7.0144813 1.5899963 18704 55 291 0 15195383 98040 11449 4209 1.4371431 66440 50 0
|
||||
44000 7.2748224 7.2748224 1.3693754 0.069498669 -0.49182853 10.347657 1.9007074 18751 73 423 0 15572639 98040 11449 4253 1.3693754 68148 50 0
|
||||
45000 5.4888002 5.4888002 1.3501677 0.050885254 -0.60200685 7.5763055 1.2841374 18662 51 314 0 15972088 98040 11449 4227 1.3501677 69998 50 0
|
||||
46000 3.2144774 3.2144774 1.3342547 0.028194354 -0.59171403 4.1978573 0.9459541 18948 50 534 0 16308430 98040 11449 4253 1.3342547 71549 50 0
|
||||
47000 4.0640905 4.0640905 1.3473081 0.036715084 -0.58898597 5.4665088 1.2043249 19188 57 236 0 16670321 98040 11449 4239 1.3473081 73216 50 0
|
||||
48000 3.7843815 3.7843815 1.3413467 0.034360184 -0.52284075 5.1158877 1.1195984 19477 57 283 0 17000588 98040 11449 4307 1.3413467 74662 50 0
|
||||
49000 4.3042567 4.3042567 1.354248 0.039635615 -0.51199566 5.9013468 1.410884 19628 68 456 0 17319627 98040 11449 4277 1.354248 75983 50 0
|
||||
50000 4.015575 4.015575 1.3058373 0.036258162 -0.58472888 5.3984778 0.84500807 19257 63 416 0 17675269 98040 11449 4254 1.3058373 77468 50 0
|
||||
Loop time of 11.9502 on 8 procs for 50000 steps with 14889 atoms
|
||||
|
||||
Pair time (%) = 1.09132 (9.13222)
|
||||
Neigh time (%) = 0.959464 (8.02883)
|
||||
Comm time (%) = 1.19057 (9.96277)
|
||||
Outpt time (%) = 0.00310364 (0.0259714)
|
||||
Other time (%) = 8.70577 (72.8502)
|
||||
|
||||
Nlocal: 1861.12 ave 1979 max 1606 min
|
||||
Histogram: 1 0 0 0 1 1 1 0 0 4
|
||||
Nghost: 35 ave 39 max 32 min
|
||||
Histogram: 1 0 2 0 3 1 0 0 0 1
|
||||
Neighs: 46 ave 61 max 31 min
|
||||
Histogram: 1 1 0 1 1 0 2 0 1 1
|
||||
|
||||
Total # of neighbors = 368
|
||||
Ave neighs/atom = 0.0247162
|
||||
Neighbor list builds = 2624
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
346
examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.g++.1
Normal file
346
examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.g++.1
Normal file
@ -0,0 +1,346 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD diffusion demo - ellipsoids
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big ellipsoidal particles
|
||||
|
||||
lattice sq 0.14
|
||||
Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for mass
|
||||
set type 1 shape 3.0 1.0 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for shape
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big quat/random 29898
|
||||
Setting atom values ...
|
||||
100 settings made for quat/random
|
||||
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute rot big temp/asphere
|
||||
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
|
||||
|
||||
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
|
||||
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
|
||||
|
||||
thermo_style custom step temp c_rot epair etotal press
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair gayberne command: doi:10.1063/1.3058435
|
||||
|
||||
@Article{Brown09,
|
||||
author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
|
||||
title = {Liquid Crystal Nanodroplets in Solution},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2009,
|
||||
volume = 130,
|
||||
number = 4,
|
||||
pages = {044901}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 13 13 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gayberne, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes
|
||||
Step Temp c_rot E_pair TotEng Press
|
||||
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
|
||||
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
|
||||
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
|
||||
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
|
||||
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
|
||||
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
|
||||
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
|
||||
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
|
||||
800 2.7632972 2.9060854 -0.52075351 2.2149107 0.7710678
|
||||
900 2.9905597 2.8869667 -0.49099378 2.4696603 0.69616841
|
||||
1000 2.8470138 2.9005012 -0.51282088 2.3057228 0.68817567
|
||||
Loop time of 0.192737 on 1 procs for 1000 steps with 100 atoms
|
||||
|
||||
Performance: 2241395.423 tau/day, 5188.415 timesteps/s, 518.842 katom-step/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 | 0.17225 | 0.17225 | 0.17225 | 0.0 | 89.37
|
||||
Neigh | 0.0025287 | 0.0025287 | 0.0025287 | 0.0 | 1.31
|
||||
Comm | 0.0023396 | 0.0023396 | 0.0023396 | 0.0 | 1.21
|
||||
Output | 0.00025405 | 0.00025405 | 0.00025405 | 0.0 | 0.13
|
||||
Modify | 0.013955 | 0.013955 | 0.013955 | 0.0 | 7.24
|
||||
Other | | 0.001413 | | | 0.73
|
||||
|
||||
Nlocal: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 77 ave 77 max 77 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 369 ave 369 max 369 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 369
|
||||
Ave neighs/atom = 3.69
|
||||
Neighbor list builds = 174
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 120.0
|
||||
Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
|
||||
create_atoms 2 region plane
|
||||
Created 85849 atoms
|
||||
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
create_atoms CPU = 0.015 seconds
|
||||
|
||||
set type 2 mass 0.01
|
||||
Setting atom values ...
|
||||
85849 settings made for mass
|
||||
group small type 2
|
||||
85849 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 2.0
|
||||
|
||||
neigh_modify one 10000
|
||||
|
||||
delete_atoms overlap 1.6 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 20 20 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 71060 atoms, new total = 14889
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/asphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press 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[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all custom 1000 dump.ellipsoid id type x y z c_0[*]
|
||||
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 14789 100
|
||||
big particle diameter max/min = 3 1
|
||||
SRD temperature & lamda = 1 0.1
|
||||
SRD max distance & max velocity = 0.4 40
|
||||
SRD grid counts: 107 107 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
|
||||
SRD per actual grid cell = 1.9275711
|
||||
SRD viscosity = 0.68810145
|
||||
big/SRD mass density ratio = 1.3736715
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 13.30933 24.335888
|
||||
ave/max big velocity = 2.0802836 5.05672
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 26.726124, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gayberne, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 43.23 | 43.23 | 43.23 Mbytes
|
||||
Step Temp c_rot f_2[9] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 2.9005012 2.9005012 0 0.025582147 -0.51282088 3.8089259 0.8986241 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.1884096 2.1884096 0.81792923 0.016786763 -0.7613492 2.4993811 1.1765894 13834 35 35 0 241 38416 11449 4172 0.81792923 16 50 0
|
||||
2000 1.2708697 1.2708697 0.90821156 0.0069438942 -0.8597194 1.0338764 0.9801188 14658 35 35 0 372 38416 11449 4281 0.90821156 16 50 0
|
||||
3000 1.1130928 1.1130928 0.9590586 0.0052557024 -0.8759868 0.78252152 0.70461705 15267 28 28 0 519 38416 11449 4292 0.9590586 16 50 0
|
||||
4000 0.8649005 0.8649005 0.9947477 0.0026217985 -0.89834217 0.39035958 0.77420962 15681 36 36 0 698 38416 11449 4339 0.9947477 16 50 0
|
||||
5000 1.1743692 1.1743692 0.98116608 0.0069116456 -0.72073526 1.0290749 0.8829165 15974 37 37 0 881 38416 11449 4328 0.98116608 16 50 0
|
||||
6000 1.0190814 1.0190814 1.0138428 0.0048088112 -0.80244733 0.7159839 0.79743882 16092 36 36 0 1090 38416 11449 4319 1.0138428 16 50 0
|
||||
7000 1.0824823 1.0824823 1.0415165 0.0049127988 -0.88143205 0.73146661 0.48157537 16178 46 46 0 1328 38416 11449 4370 1.0415165 23 50 0
|
||||
8000 1.0482457 1.0482457 1.0336952 0.0051802902 -0.79059275 0.7712934 0.75744414 16622 33 33 0 1579 38416 11449 4340 1.0336952 24 50 0
|
||||
9000 0.98889815 0.98889815 1.0126005 0.00397567 -0.88152073 0.59193751 0.52056685 16877 41 41 0 1811 38416 11449 4370 1.0126005 27 50 0
|
||||
10000 0.96559538 0.96559538 1.0234124 0.0045683795 -0.7585511 0.68018602 0.70666049 16833 32 32 0 2038 38416 11449 4330 1.0234124 27 50 0
|
||||
Loop time of 9.04639 on 1 procs for 10000 steps with 14889 atoms
|
||||
|
||||
Performance: 47753.873 tau/day, 1105.414 timesteps/s, 16.459 Matom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.862 | 1.862 | 1.862 | 0.0 | 20.58
|
||||
Neigh | 0.018395 | 0.018395 | 0.018395 | 0.0 | 0.20
|
||||
Comm | 0.060502 | 0.060502 | 0.060502 | 0.0 | 0.67
|
||||
Output | 0.00092704 | 0.00092704 | 0.00092704 | 0.0 | 0.01
|
||||
Modify | 7.0482 | 7.0482 | 7.0482 | 0.0 | 77.91
|
||||
Other | | 0.05636 | | | 0.62
|
||||
|
||||
Nlocal: 14889 ave 14889 max 14889 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 79 ave 79 max 79 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 416 ave 416 max 416 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 416
|
||||
Ave neighs/atom = 0.02794009
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:11
|
||||
346
examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.g++.4
Normal file
346
examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.g++.4
Normal file
@ -0,0 +1,346 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD diffusion demo - ellipsoids
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big ellipsoidal particles
|
||||
|
||||
lattice sq 0.14
|
||||
Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for mass
|
||||
set type 1 shape 3.0 1.0 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for shape
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big quat/random 29898
|
||||
Setting atom values ...
|
||||
100 settings made for quat/random
|
||||
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute rot big temp/asphere
|
||||
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
|
||||
|
||||
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
|
||||
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
|
||||
|
||||
thermo_style custom step temp c_rot epair etotal press
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair gayberne command: doi:10.1063/1.3058435
|
||||
|
||||
@Article{Brown09,
|
||||
author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
|
||||
title = {Liquid Crystal Nanodroplets in Solution},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2009,
|
||||
volume = 130,
|
||||
number = 4,
|
||||
pages = {044901}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 13 13 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gayberne, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
|
||||
Step Temp c_rot E_pair TotEng Press
|
||||
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
|
||||
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
|
||||
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
|
||||
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
|
||||
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
|
||||
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
|
||||
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
|
||||
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
|
||||
800 2.7632972 2.9060855 -0.52075354 2.2149107 0.77106773
|
||||
900 2.9905599 2.8869667 -0.49099386 2.4696604 0.69616823
|
||||
1000 2.8470131 2.9005016 -0.51282147 2.3057215 0.68817329
|
||||
Loop time of 0.0666302 on 4 procs for 1000 steps with 100 atoms
|
||||
|
||||
Performance: 6483542.632 tau/day, 15008.201 timesteps/s, 1.501 Matom-step/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.039208 | 0.042833 | 0.045871 | 1.2 | 64.29
|
||||
Neigh | 0.00065929 | 0.00071982 | 0.00076852 | 0.0 | 1.08
|
||||
Comm | 0.013998 | 0.017169 | 0.02087 | 1.9 | 25.77
|
||||
Output | 0.00018817 | 0.00020663 | 0.00025962 | 0.0 | 0.31
|
||||
Modify | 0.0035046 | 0.0035933 | 0.003701 | 0.1 | 5.39
|
||||
Other | | 0.002109 | | | 3.16
|
||||
|
||||
Nlocal: 25 ave 27 max 24 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 42.25 ave 45 max 38 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Neighs: 92.25 ave 104 max 85 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 369
|
||||
Ave neighs/atom = 3.69
|
||||
Neighbor list builds = 174
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 120.0
|
||||
Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
|
||||
create_atoms 2 region plane
|
||||
Created 85849 atoms
|
||||
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
create_atoms CPU = 0.004 seconds
|
||||
|
||||
set type 2 mass 0.01
|
||||
Setting atom values ...
|
||||
85849 settings made for mass
|
||||
group small type 2
|
||||
85849 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 2.0
|
||||
|
||||
neigh_modify one 10000
|
||||
|
||||
delete_atoms overlap 1.6 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 20 20 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 71060 atoms, new total = 14889
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/asphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press 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[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all custom 1000 dump.ellipsoid id type x y z c_0[*]
|
||||
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 14789 100
|
||||
big particle diameter max/min = 3 1
|
||||
SRD temperature & lamda = 1 0.1
|
||||
SRD max distance & max velocity = 0.4 40
|
||||
SRD grid counts: 107 107 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
|
||||
SRD per actual grid cell = 1.9275711
|
||||
SRD viscosity = 0.68810145
|
||||
big/SRD mass density ratio = 1.3736715
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 13.30933 24.335888
|
||||
ave/max big velocity = 2.080284 5.0567191
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 26.726124, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gayberne, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.89 | 16.9 | 16.91 Mbytes
|
||||
Step Temp c_rot f_2[9] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 2.9005016 2.9005016 0 0.025582147 -0.51282147 3.8089259 0.89862191 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.7138279 2.7138279 0.82437872 0.023781703 -0.50274582 3.5408578 1.6816604 13758 32 34 0 274 66564 11449 4238 0.82437872 24 50 0
|
||||
2000 1.3183118 1.3183118 0.91362053 0.0077748292 -0.80669023 1.1575943 1.1678425 14118 23 23 0 414 66564 11449 4269 0.91362053 24 50 0
|
||||
3000 1.3117991 1.3117991 0.96889539 0.0065133847 -0.98480276 0.96977785 0.51801823 14675 35 36 0 588 66564 11449 4291 0.96889539 26 50 0
|
||||
4000 1.1034132 1.1034132 0.95899765 0.0042496304 -1.0113582 0.63272747 0.6382343 15146 38 38 0 776 66564 11449 4309 0.95899765 26 50 0
|
||||
5000 1.0814177 1.0814177 1.0037423 0.0047549676 -0.90334518 0.70796713 0.76138491 15275 40 40 0 973 66564 11449 4285 1.0037423 26 50 0
|
||||
6000 1.0515425 1.0515425 0.98728204 0.0041039749 -0.95575757 0.61104083 0.61253791 15685 34 34 0 1205 66564 11449 4328 0.98728204 26 50 0
|
||||
7000 0.96229389 0.96229389 1.0146054 0.0031968892 -0.95783307 0.47598483 0.4469161 15944 43 43 0 1412 66564 11449 4391 1.0146054 27 50 0
|
||||
8000 0.98798058 0.98798058 0.99692702 0.0037348841 -0.91600418 0.55608689 0.50558822 16250 43 43 0 1637 66564 11449 4330 0.99692702 27 50 0
|
||||
9000 1.0120554 1.0120554 1.0099521 0.0039518454 -0.91957229 0.58839026 0.4092229 16367 43 44 0 1899 66564 11449 4309 1.0099521 27 50 0
|
||||
10000 1.104152 1.104152 0.9993147 0.0053713858 -0.84544079 0.79974564 0.5119979 16331 50 50 0 2108 66564 11449 4353 0.9993147 27 50 0
|
||||
Loop time of 2.95619 on 4 procs for 10000 steps with 14889 atoms
|
||||
|
||||
Performance: 146134.205 tau/day, 3382.736 timesteps/s, 50.366 Matom-step/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 | 0.48773 | 0.52727 | 0.62879 | 8.1 | 17.84
|
||||
Neigh | 0.0070094 | 0.0072204 | 0.0076255 | 0.3 | 0.24
|
||||
Comm | 0.12898 | 0.22553 | 0.265 | 11.8 | 7.63
|
||||
Output | 0.0005957 | 0.00064777 | 0.00075264 | 0.0 | 0.02
|
||||
Modify | 2.1317 | 2.1512 | 2.166 | 0.9 | 72.77
|
||||
Other | | 0.04427 | | | 1.50
|
||||
|
||||
Nlocal: 3722.25 ave 3968 max 3389 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 39.75 ave 44 max 35 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 101 ave 125 max 86 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 404
|
||||
Ave neighs/atom = 0.027134126
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
347
examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.mp.g++.1
Normal file
347
examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.mp.g++.1
Normal file
@ -0,0 +1,347 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD viscosity demo - ellipsoids
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big ellipsoidal particles
|
||||
|
||||
lattice sq 0.14
|
||||
Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for mass
|
||||
set type 1 shape 3.0 1.0 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for shape
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big quat/random 29898
|
||||
Setting atom values ...
|
||||
100 settings made for quat/random
|
||||
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute rot big temp/asphere
|
||||
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
|
||||
|
||||
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
|
||||
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
|
||||
|
||||
thermo_style custom step temp c_rot epair etotal press
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair gayberne command: doi:10.1063/1.3058435
|
||||
|
||||
@Article{Brown09,
|
||||
author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
|
||||
title = {Liquid Crystal Nanodroplets in Solution},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2009,
|
||||
volume = 130,
|
||||
number = 4,
|
||||
pages = {044901}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 13 13 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gayberne, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes
|
||||
Step Temp c_rot E_pair TotEng Press
|
||||
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
|
||||
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
|
||||
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
|
||||
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
|
||||
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
|
||||
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
|
||||
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
|
||||
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
|
||||
800 2.7632972 2.9060854 -0.52075351 2.2149107 0.7710678
|
||||
900 2.9905597 2.8869667 -0.49099378 2.4696603 0.69616841
|
||||
1000 2.8470138 2.9005012 -0.51282088 2.3057228 0.68817567
|
||||
Loop time of 0.192844 on 1 procs for 1000 steps with 100 atoms
|
||||
|
||||
Performance: 2240155.241 tau/day, 5185.545 timesteps/s, 518.554 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17225 | 0.17225 | 0.17225 | 0.0 | 89.32
|
||||
Neigh | 0.0025614 | 0.0025614 | 0.0025614 | 0.0 | 1.33
|
||||
Comm | 0.0024746 | 0.0024746 | 0.0024746 | 0.0 | 1.28
|
||||
Output | 0.0001406 | 0.0001406 | 0.0001406 | 0.0 | 0.07
|
||||
Modify | 0.014112 | 0.014112 | 0.014112 | 0.0 | 7.32
|
||||
Other | | 0.001306 | | | 0.68
|
||||
|
||||
Nlocal: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 77 ave 77 max 77 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 369 ave 369 max 369 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 369
|
||||
Ave neighs/atom = 3.69
|
||||
Neighbor list builds = 174
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 120.0
|
||||
Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
|
||||
create_atoms 2 region plane
|
||||
Created 85849 atoms
|
||||
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
create_atoms CPU = 0.015 seconds
|
||||
|
||||
set type 2 mass 0.01
|
||||
Setting atom values ...
|
||||
85849 settings made for mass
|
||||
group small type 2
|
||||
85849 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 2.0
|
||||
|
||||
neigh_modify one 10000
|
||||
|
||||
delete_atoms overlap 1.6 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 20 20 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 71060 atoms, new total = 14889
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
|
||||
fix 3 small viscosity 20 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/asphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press 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[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all custom 500 dump.ellipsoid id type x y z c_0[*]
|
||||
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 14789 100
|
||||
big particle diameter max/min = 3 1
|
||||
SRD temperature & lamda = 1 0.1
|
||||
SRD max distance & max velocity = 0.4 40
|
||||
SRD grid counts: 107 107 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
|
||||
SRD per actual grid cell = 1.9275711
|
||||
SRD viscosity = 0.68810145
|
||||
big/SRD mass density ratio = 1.3736715
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 13.30933 24.335888
|
||||
ave/max big velocity = 2.0802836 5.05672
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 26.726124, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gayberne, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 43.23 | 43.23 | 43.23 Mbytes
|
||||
Step Temp c_rot f_2[9] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 2.9005012 2.9005012 0 0.025582147 -0.51282088 3.8089259 0.8986241 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.3102693 2.3102693 0.82371999 0.019779507 -0.49733043 2.9449709 1.9807143 13954 30 30 0 277 38416 11449 4255 0.82371999 15 50 0
|
||||
2000 1.5312119 1.5312119 0.90846884 0.008532096 -1.011162 1.2703438 0.58038663 14523 37 37 0 439 38416 11449 4257 0.90846884 20 50 0
|
||||
3000 1.3603443 1.3603443 0.95241399 0.0085403252 -0.75534393 1.271569 1.2262133 14864 34 35 0 599 38416 11449 4287 0.95241399 20 50 0
|
||||
4000 2.2408861 2.2408861 0.99089404 0.016876315 -0.82620566 2.5127146 1.2664088 15457 35 35 0 809 38416 11449 4272 0.99089404 21 50 0
|
||||
5000 1.7110067 1.7110067 0.99729333 0.011146301 -0.88982716 1.6595728 0.97334407 15555 36 36 0 1026 38416 11449 4324 0.99729333 24 50 0
|
||||
6000 1.684666 1.684666 1.0235606 0.009751253 -1.0582882 1.4518641 0.62435255 15752 45 46 0 1256 38416 11449 4303 1.0235606 24 50 0
|
||||
7000 2.1142261 2.1142261 1.0160206 0.014786886 -0.94857757 2.2016194 0.7761903 16144 30 30 0 1492 38416 11449 4401 1.0160206 27 50 0
|
||||
8000 2.5622926 2.5622926 1.0125365 0.019933518 -0.84991443 2.9679015 0.93716383 16302 43 43 0 1720 38416 11449 4346 1.0125365 27 50 0
|
||||
9000 2.6593623 2.6593623 1.0110535 0.020725053 -0.87669675 3.0857531 0.97818336 16856 44 44 0 2000 38416 11449 4298 1.0110535 30 50 0
|
||||
10000 2.7567851 2.7567851 1.0379053 0.021598993 -0.8917358 3.2158741 0.74950846 16770 50 53 0 2284 38416 11449 4316 1.0379053 30 50 0
|
||||
Loop time of 9.02679 on 1 procs for 10000 steps with 14889 atoms
|
||||
|
||||
Performance: 47857.551 tau/day, 1107.814 timesteps/s, 16.494 Matom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.8454 | 1.8454 | 1.8454 | 0.0 | 20.44
|
||||
Neigh | 0.018708 | 0.018708 | 0.018708 | 0.0 | 0.21
|
||||
Comm | 0.059853 | 0.059853 | 0.059853 | 0.0 | 0.66
|
||||
Output | 0.00081453 | 0.00081453 | 0.00081453 | 0.0 | 0.01
|
||||
Modify | 7.0469 | 7.0469 | 7.0469 | 0.0 | 78.07
|
||||
Other | | 0.05507 | | | 0.61
|
||||
|
||||
Nlocal: 14889 ave 14889 max 14889 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 75 ave 75 max 75 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 382 ave 382 max 382 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 382
|
||||
Ave neighs/atom = 0.025656525
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:11
|
||||
347
examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.mp.g++.4
Normal file
347
examples/ASPHERE/ellipsoid/log.1Feb24.ellipsoid.mp.g++.4
Normal file
@ -0,0 +1,347 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD viscosity demo - ellipsoids
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big ellipsoidal particles
|
||||
|
||||
lattice sq 0.14
|
||||
Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for mass
|
||||
set type 1 shape 3.0 1.0 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for shape
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big quat/random 29898
|
||||
Setting atom values ...
|
||||
100 settings made for quat/random
|
||||
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute rot big temp/asphere
|
||||
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
|
||||
|
||||
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
|
||||
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
|
||||
|
||||
thermo_style custom step temp c_rot epair etotal press
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- pair gayberne command: doi:10.1063/1.3058435
|
||||
|
||||
@Article{Brown09,
|
||||
author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
|
||||
title = {Liquid Crystal Nanodroplets in Solution},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2009,
|
||||
volume = 130,
|
||||
number = 4,
|
||||
pages = {044901}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 13 13 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gayberne, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
|
||||
Step Temp c_rot E_pair TotEng Press
|
||||
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
|
||||
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
|
||||
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
|
||||
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
|
||||
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
|
||||
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
|
||||
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
|
||||
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
|
||||
800 2.7632972 2.9060855 -0.52075354 2.2149107 0.77106773
|
||||
900 2.9905599 2.8869667 -0.49099386 2.4696604 0.69616823
|
||||
1000 2.8470131 2.9005016 -0.51282147 2.3057215 0.68817329
|
||||
Loop time of 0.0905036 on 4 procs for 1000 steps with 100 atoms
|
||||
|
||||
Performance: 4773291.472 tau/day, 11049.286 timesteps/s, 1.105 Matom-step/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 | 0.039039 | 0.053443 | 0.065528 | 5.0 | 59.05
|
||||
Neigh | 0.00068257 | 0.00086692 | 0.0010442 | 0.0 | 0.96
|
||||
Comm | 0.016567 | 0.028689 | 0.043189 | 6.8 | 31.70
|
||||
Output | 0.00016989 | 0.00018594 | 0.0002316 | 0.0 | 0.21
|
||||
Modify | 0.0035809 | 0.0043052 | 0.0050755 | 1.0 | 4.76
|
||||
Other | | 0.003013 | | | 3.33
|
||||
|
||||
Nlocal: 25 ave 27 max 24 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 42.25 ave 45 max 38 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Neighs: 92.25 ave 104 max 85 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 369
|
||||
Ave neighs/atom = 3.69
|
||||
Neighbor list builds = 174
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 120.0
|
||||
Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
|
||||
create_atoms 2 region plane
|
||||
Created 85849 atoms
|
||||
using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
|
||||
create_atoms CPU = 0.007 seconds
|
||||
|
||||
set type 2 mass 0.01
|
||||
Setting atom values ...
|
||||
85849 settings made for mass
|
||||
group small type 2
|
||||
85849 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 2.0
|
||||
|
||||
neigh_modify one 10000
|
||||
|
||||
delete_atoms overlap 1.6 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 20 20 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 71060 atoms, new total = 14889
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
|
||||
fix 3 small viscosity 20 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/asphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press 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[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all custom 500 dump.ellipsoid id type x y z c_0[*]
|
||||
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 14789 100
|
||||
big particle diameter max/min = 3 1
|
||||
SRD temperature & lamda = 1 0.1
|
||||
SRD max distance & max velocity = 0.4 40
|
||||
SRD grid counts: 107 107 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
|
||||
SRD per actual grid cell = 1.9275711
|
||||
SRD viscosity = 0.68810145
|
||||
big/SRD mass density ratio = 1.3736715
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 13.30933 24.335888
|
||||
ave/max big velocity = 2.080284 5.0567191
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 10000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 26.726124, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gayberne, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.89 | 16.9 | 16.91 Mbytes
|
||||
Step Temp c_rot f_2[9] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 2.9005016 2.9005016 0 0.025582147 -0.51282147 3.8089259 0.89862191 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 2.5269102 2.5269102 0.8207596 0.022784455 -0.37271861 3.3923775 2.0963085 13925 34 34 0 322 66564 11449 4235 0.8207596 24 50 0
|
||||
2000 1.3685596 1.3685596 0.89115879 0.0089112146 -0.71236311 1.3267907 1.3970875 14444 25 25 0 454 66564 11449 4278 0.89115879 25 50 0
|
||||
3000 1.5234001 1.5234001 0.9828293 0.0090168318 -0.92735003 1.3425161 0.70104224 14946 37 37 0 608 66564 11449 4331 0.9828293 27 50 0
|
||||
4000 2.2536932 2.2536932 0.97648579 0.017005211 -0.82609701 2.5319058 1.190307 15428 43 43 0 827 66564 11449 4346 0.97648579 32 50 0
|
||||
5000 1.8106358 1.8106358 1.0143347 0.012032652 -0.90630586 1.7915415 0.83451531 15438 26 26 0 1039 66564 11449 4314 1.0143347 32 50 0
|
||||
6000 1.9880605 1.9880605 1.0142917 0.013767418 -0.91237924 2.0498309 0.87383026 15688 37 37 0 1279 66564 11449 4353 1.0142917 32 50 0
|
||||
7000 2.4772098 2.4772098 0.99457682 0.018062012 -1.0017896 2.689253 0.74369504 15723 38 38 0 1521 66564 11449 4293 0.99457682 32 50 0
|
||||
8000 2.5749419 2.5749419 1.0337514 0.019908918 -0.87242464 2.9642389 1.0460672 15932 33 34 0 1805 66564 11449 4320 1.0337514 32 50 0
|
||||
9000 2.4877578 2.4877578 1.0366259 0.019125113 -0.85922105 2.847538 0.95616808 16292 52 53 0 2099 66564 11449 4291 1.0366259 33 50 0
|
||||
10000 2.8498311 2.8498311 1.0117104 0.022669267 -0.87102125 3.3752271 0.98313087 16736 38 38 0 2415 66564 11449 4366 1.0117104 35 50 0
|
||||
Loop time of 3.0339 on 4 procs for 10000 steps with 14889 atoms
|
||||
|
||||
Performance: 142390.919 tau/day, 3296.086 timesteps/s, 49.075 Matom-step/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.46168 | 0.52303 | 0.69055 | 13.4 | 17.24
|
||||
Neigh | 0.0068493 | 0.0072892 | 0.0081958 | 0.6 | 0.24
|
||||
Comm | 0.12806 | 0.2911 | 0.34961 | 17.5 | 9.59
|
||||
Output | 0.00055286 | 0.00057977 | 0.00065772 | 0.0 | 0.02
|
||||
Modify | 2.1454 | 2.1674 | 2.1833 | 0.9 | 71.44
|
||||
Other | | 0.04447 | | | 1.47
|
||||
|
||||
Nlocal: 3722.25 ave 4163 max 3210 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 46.25 ave 49 max 43 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Neighs: 102.5 ave 143 max 79 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 410
|
||||
Ave neighs/atom = 0.027537108
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -1,44 +1,44 @@
|
||||
# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent
|
||||
|
||||
units lj
|
||||
atom_style line
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style line
|
||||
dimension 2
|
||||
|
||||
read_data data.line
|
||||
read_data data.line
|
||||
|
||||
velocity all create 1.44 320984 loop geom
|
||||
velocity all create 1.44 320984 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule/intra all
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule/intra all
|
||||
|
||||
pair_style line/lj 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0 0.25 2.5
|
||||
pair_style line/lj 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0 0.25 2.5
|
||||
|
||||
fix 2 all rigid molecule langevin 2.0 2.0 1.0 492983
|
||||
fix 2 all rigid molecule langevin 2.0 2.0 1.0 492983
|
||||
|
||||
fix 3 all deform 1 x scale 0.3 y scale 0.3
|
||||
fix 4 all enforce2d
|
||||
fix 3 all deform 1 x scale 0.3 y scale 0.3
|
||||
fix 4 all enforce2d
|
||||
|
||||
compute 10 all property/atom end1x end1y end2x end2y
|
||||
compute 10 all property/atom end1x end1y end2x end2y
|
||||
|
||||
#dump 1 all custom 500 dump1.atom id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.line id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
#dump 1 all custom 500 dump1.atom id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.line id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
timestep 0.004
|
||||
timestep 0.004
|
||||
|
||||
compute 1 all erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
compute 1 all erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
compute_modify thermo_temp extra/dof -350
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step f_2 pe ke c_1 c_2 c_3 v_toteng
|
||||
thermo 1000
|
||||
thermo_style custom step f_2 pe ke c_1 c_2 c_3 v_toteng
|
||||
|
||||
run 10000
|
||||
run 10000
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
@ -46,10 +46,10 @@ unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
|
||||
#dump 1 all custom 500 dump2.atom id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.line id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
#dump 1 all custom 500 dump2.atom id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.line id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.01 units box
|
||||
fix 3 all deform 1 xy erate 0.01 units box
|
||||
|
||||
run 100000
|
||||
run 10000
|
||||
|
||||
@ -1,107 +1,107 @@
|
||||
# Aspherical shear demo - 2d line boxes, solvated by SRD particles
|
||||
|
||||
units lj
|
||||
atom_style line
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style line
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
read_data data.line.srd
|
||||
read_data data.line.srd
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sq 0.4
|
||||
region plane block INF INF INF INF -0.001 0.001
|
||||
lattice sq 10.0
|
||||
create_atoms 2 region plane
|
||||
lattice sq 0.4
|
||||
region plane block INF INF INF INF -0.001 0.001
|
||||
lattice sq 10.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
group big type 1
|
||||
group small type 2
|
||||
set group small mass 0.01
|
||||
group big type 1
|
||||
group small type 2
|
||||
set group small mass 0.01
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
delete_atoms overlap 1.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule/intra big include big
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule/intra big include big
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style line/lj 2.5
|
||||
pair_coeff 1 1 1.0 1.0 1.0 1.0 2.5
|
||||
pair_coeff 2 2 0.0 0.0 0.0 1.0 0.0
|
||||
pair_coeff 1 2 1.0 0.0 0.0 1.0 0.0
|
||||
pair_style line/lj 2.5
|
||||
pair_coeff 1 1 1.0 1.0 1.0 1.0 2.5
|
||||
pair_coeff 2 2 0.0 0.0 0.0 1.0 0.0
|
||||
pair_coeff 1 2 1.0 0.0 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip
|
||||
|
||||
fix 3 all deform 1 x scale 0.35 y scale 0.35
|
||||
fix 4 all enforce2d
|
||||
fix 3 all deform 1 x scale 0.35 y scale 0.35
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute_modify tbig extra/dof -350
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step c_tsmall f_2[9] c_1 etotal &
|
||||
v_pebig v_ebig press
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
thermo_style custom step c_tsmall f_2[9] c_1 etotal &
|
||||
v_pebig v_ebig press
|
||||
thermo_modify temp tbig
|
||||
|
||||
compute 10 big property/atom end1x end1y end2x end2y
|
||||
compute 10 big property/atom end1x end1y end2x end2y
|
||||
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.line.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.line.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
run 10000
|
||||
run 10000
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip tstat yes
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip tstat yes
|
||||
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.line.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.line.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 40000
|
||||
run 40000
|
||||
|
||||
@ -1,114 +1,114 @@
|
||||
# SRD diffusion demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
create_atoms 1 region box
|
||||
lattice sq 0.3
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
create_atoms 1 region box
|
||||
|
||||
group big type 1
|
||||
set group big type/fraction 2 0.33 394895
|
||||
set group big type/fraction 3 0.5 989894
|
||||
group big type 2 3
|
||||
group big type 1
|
||||
set group big type/fraction 2 0.33 394895
|
||||
set group big type/fraction 3 0.5 989894
|
||||
group big type 2 3
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
velocity big create 1.44 87287 loop geom
|
||||
set type 1*3 mass 1.0
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
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
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
create_atoms 4 region plane
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
create_atoms 4 region plane
|
||||
|
||||
set type 4 mass 0.1
|
||||
group small type 4
|
||||
velocity small create 1.0 593849 loop geom
|
||||
set type 4 mass 0.1
|
||||
group small type 4
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
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
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
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
|
||||
|
||||
reset_timestep 0
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 inside ignore
|
||||
fix 3 all enforce2d
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
thermo_modify temp tbig
|
||||
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_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
|
||||
#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
|
||||
|
||||
run 100000
|
||||
run 10000
|
||||
|
||||
@ -1,115 +1,115 @@
|
||||
# SRD viscosity demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
create_atoms 1 region box
|
||||
lattice sq 0.3
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
create_atoms 1 region box
|
||||
|
||||
group big type 1
|
||||
set group big type/fraction 2 0.33 394895
|
||||
set group big type/fraction 3 0.5 989894
|
||||
group big type 2 3
|
||||
group big type 1
|
||||
set group big type/fraction 2 0.33 394895
|
||||
set group big type/fraction 3 0.5 989894
|
||||
group big type 2 3
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
velocity big create 1.44 87287 loop geom
|
||||
set type 1*3 mass 1.0
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
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
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
create_atoms 4 region plane
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
create_atoms 4 region plane
|
||||
|
||||
set type 4 mass 0.1
|
||||
group small type 4
|
||||
velocity small create 1.0 593849 loop geom
|
||||
set type 4 mass 0.1
|
||||
group small type 4
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
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
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
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
|
||||
|
||||
reset_timestep 0
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 inside ignore
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 inside ignore
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
thermo_modify temp tbig
|
||||
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_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
|
||||
#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
|
||||
|
||||
run 50000
|
||||
run 10000
|
||||
|
||||
@ -1,288 +0,0 @@
|
||||
LAMMPS (1 Feb 2014)
|
||||
# SRD diffusion demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
Created orthogonal box = (0 0 -0.912871) to (18.2574 18.2574 0.912871)
|
||||
2 by 4 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big type/fraction 2 0.33 394895
|
||||
35 settings made for type/fraction
|
||||
set group big type/fraction 3 0.5 989894
|
||||
57 settings made for type/fraction
|
||||
group big type 2 3
|
||||
100 atoms in group big
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
100 settings made for mass
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 2.7472 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.16013916 0 1.2654608 1.1298975
|
||||
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
|
||||
Loop time of 0.0221665 on 8 procs for 1000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 0.000323534 (1.45957)
|
||||
Neigh time (%) = 0.000274181 (1.23692)
|
||||
Comm time (%) = 0.0146933 (66.2864)
|
||||
Outpt time (%) = 2.864e-05 (0.129204)
|
||||
Other time (%) = 0.00684676 (30.8879)
|
||||
|
||||
Nlocal: 12.5 ave 18 max 10 min
|
||||
Histogram: 1 3 1 1 0 1 0 0 0 1
|
||||
Nghost: 27.75 ave 31 max 24 min
|
||||
Histogram: 1 0 1 0 2 2 0 0 0 2
|
||||
Neighs: 19 ave 30 max 16 min
|
||||
Histogram: 4 1 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 152
|
||||
Ave neighs/atom = 1.52
|
||||
Neighbor list builds = 115
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
Lattice spacing in x,y,z = 0.0632456 0.0632456 0.0632456
|
||||
create_atoms 4 region plane
|
||||
Created 83521 atoms
|
||||
|
||||
set type 4 mass 0.1
|
||||
83521 settings made for mass
|
||||
group small type 4
|
||||
83521 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
pair_coeff 2 4 0.0 1.0 1.0
|
||||
pair_coeff 3 4 0.0 1.0 0.75
|
||||
|
||||
delete_atoms overlap 1.0 small big
|
||||
Deleted 63410 atoms, new total = 20211
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.poly
|
||||
|
||||
#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
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 20111 100
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 73 73 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250102 0.250102 1.82574
|
||||
SRD per actual grid cell = 4.93717
|
||||
SRD viscosity = 0.23322
|
||||
big/SRD mass density ratio = 0.161311
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.19344 7.74495
|
||||
ave/max big velocity = 1.43991 3.5724
|
||||
Memory usage per processor = 11.8633 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11]
|
||||
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 0.84607633 3934 0.0065245151 0.058016014 1.3186697 4.2649214 7470 26 26 0 665 36480 5329 3934 0.95810956 0 2
|
||||
2000 0.86586785 3944 0.0045898954 -0.36247933 0.92766376 2.1563866 7786 30 30 0 1374 36480 5329 3944 1.0799777 0 49
|
||||
3000 0.78968677 4001 0.00417319 -0.33318986 0.84344343 1.9302042 7957 34 34 0 2129 36480 5329 4001 1.1247747 0 49
|
||||
4000 0.7110667 4005 0.0031642256 -0.41996775 0.63952164 1.9679689 8188 24 24 0 2925 36480 5329 4005 1.1345941 0 49
|
||||
5000 0.80379425 4052 0.0038912991 -0.41118297 0.78647047 1.6851034 8326 30 30 0 3794 36480 5329 4052 1.1310774 0 49
|
||||
6000 0.96927432 4048 0.0054656969 -0.33954674 1.104672 1.8976158 8380 23 23 0 4643 36480 5329 4048 1.1861264 0 49
|
||||
7000 0.75821666 4050 0.0036201309 -0.39807817 0.73166465 1.6087451 8450 51 51 0 5699 36480 5329 4050 1.1664119 0 49
|
||||
8000 0.8712338 4035 0.0047243103 -0.343308 0.95483036 1.4707918 8458 42 42 0 6974 36480 5329 4035 1.1947807 0 91
|
||||
9000 0.87995969 4048 0.0042778416 -0.44654537 0.86459457 1.5567027 8379 36 36 0 7965 36480 5329 4048 1.1675384 0 91
|
||||
10000 0.83009098 4053 0.0042178709 -0.38436167 0.85247389 1.9119485 8373 34 34 0 8952 36480 5329 4053 1.1933986 0 91
|
||||
11000 0.73595909 4015 0.0037439098 -0.33989742 0.75668162 1.6495307 8333 22 22 0 9983 36480 5329 4015 1.1959519 0 91
|
||||
12000 0.84043443 4034 0.0041823741 -0.40694768 0.84529962 1.5115578 8566 31 31 0 11023 36480 5329 4034 1.2064988 0 91
|
||||
13000 0.64253331 4044 0.0034868675 -0.25264383 0.7047308 1.739124 8528 31 31 0 12101 36480 5329 4044 1.1912336 0 91
|
||||
14000 0.99330171 4042 0.0055047339 -0.36745778 1.1125618 1.8215191 8548 36 36 0 13098 36480 5329 4042 1.1819124 0 91
|
||||
15000 0.90379859 4049 0.0049047446 -0.35536197 0.99129793 1.7159536 8459 37 37 0 14130 36480 5329 4049 1.1806762 0 91
|
||||
16000 0.87446498 4034 0.0053318245 -0.22533777 1.0776151 2.0239395 8690 33 33 0 15176 36480 5329 4034 1.1912858 0 91
|
||||
17000 0.95733995 4035 0.0053759665 -0.33989994 1.0865366 1.6243881 8518 27 27 0 16147 36480 5329 4035 1.2074487 0 91
|
||||
18000 1.03543 4032 0.0052946469 -0.47268961 1.0701011 1.5444562 8464 28 28 0 17230 36480 5329 4032 1.1959755 0 91
|
||||
19000 0.75997582 4051 0.0034371936 -0.43767278 0.6946912 1.4209137 8436 39 39 0 18276 36480 5329 4051 1.182461 0 91
|
||||
20000 0.89615234 4037 0.0048910458 -0.34673773 0.98852926 1.5843879 8433 28 28 0 19275 36480 5329 4037 1.1850673 0 91
|
||||
21000 0.85849578 4063 0.0044978314 -0.37010201 0.9090567 1.5445809 8504 40 40 0 20278 36480 5329 4063 1.1931031 0 91
|
||||
22000 0.79050471 4066 0.0038260812 -0.40456274 0.77328927 1.6214277 8463 44 44 0 21287 36480 5329 4066 1.1948824 0 91
|
||||
23000 0.89563532 4026 0.0051030186 -0.30312555 1.0313711 1.4848223 8548 35 35 0 22422 36480 5329 4026 1.1975081 0 91
|
||||
24000 0.83528717 4036 0.0043136275 -0.37275064 0.87182725 1.5504059 8527 34 34 0 23404 36480 5329 4036 1.1755463 0 91
|
||||
25000 0.64179358 4022 0.0035185741 -0.24513342 0.71113901 1.7238889 8452 47 47 0 24522 36480 5329 4022 1.2066339 0 91
|
||||
26000 0.86710098 4028 0.0046099591 -0.36026164 0.93171883 1.4255297 8734 33 33 0 25524 36480 5329 4028 1.2001233 0 91
|
||||
27000 0.8327003 4054 0.0045323379 -0.32469262 0.91603082 1.2654649 8468 34 34 0 26520 36480 5329 4054 1.1814901 0 91
|
||||
28000 0.84396759 4049 0.0042805934 -0.39236096 0.86515074 1.2929473 8536 37 37 0 27657 36480 5329 4049 1.1897647 0 91
|
||||
29000 0.77639299 4052 0.0038143413 -0.38590904 0.77091652 1.3627099 8637 36 36 0 28773 36480 5329 4052 1.1858017 0 91
|
||||
30000 0.69994805 4046 0.0034430868 -0.34704032 0.69588228 1.5351247 8704 46 46 0 29818 36480 5329 4046 1.1724555 0 91
|
||||
31000 0.73907898 4039 0.003034759 -0.48787254 0.61335514 1.2291035 8486 29 29 0 30848 36480 5329 4039 1.2063852 0 91
|
||||
32000 0.84649298 4052 0.0044326201 -0.36539769 0.89587685 1.4591662 8513 28 28 0 31917 36480 5329 4052 1.1917883 0 91
|
||||
33000 0.7188891 4031 0.0033440675 -0.39527528 0.67586949 1.2495703 8800 37 37 0 32938 36480 5329 4031 1.191087 0 91
|
||||
34000 0.93588921 4054 0.0054112843 -0.30080024 1.0936747 1.3650172 8585 33 33 0 33913 36480 5329 4054 1.1840415 0 91
|
||||
35000 0.86446961 4039 0.0053251497 -0.21179371 1.076266 1.3791947 8607 22 22 0 34865 36480 5329 4039 1.1916342 0 91
|
||||
36000 0.90510006 4011 0.0054168442 -0.2538007 1.0947984 1.5747653 8479 31 31 0 35842 36480 5329 4011 1.1760305 0 91
|
||||
37000 0.95332175 4058 0.0055020495 -0.30843018 1.1120192 1.4326924 8512 29 29 0 36751 36480 5329 4058 1.180738 0 91
|
||||
38000 0.71413841 4043 0.0038380378 -0.2883604 0.77570582 1.4283837 8611 39 39 0 37689 36480 5329 4043 1.1693806 0 91
|
||||
39000 0.81161335 4064 0.0044323475 -0.31348213 0.89582176 1.4378305 8697 28 28 0 38696 36480 5329 4064 1.1987209 0 91
|
||||
40000 0.8294437 4062 0.0051262098 -0.19981285 1.0360583 1.6010501 8559 31 31 0 39743 36480 5329 4062 1.2092371 0 91
|
||||
41000 0.79325147 4079 0.0045273868 -0.26691453 0.91503015 1.4080428 8775 53 53 0 40806 36480 5329 4079 1.1989619 0 91
|
||||
42000 0.95693891 4027 0.005623893 -0.28919396 1.136645 1.5334192 8509 34 34 0 41793 36480 5329 4027 1.1931035 0 91
|
||||
43000 0.66458435 4029 0.0035902162 -0.26461209 0.72561859 1.4253918 8559 44 44 0 42768 36480 5329 4029 1.2111853 0 91
|
||||
44000 0.84442459 4022 0.0050980388 -0.22782802 1.0303646 1.4587515 8522 32 32 0 43812 36480 5329 4022 1.1943268 0 91
|
||||
45000 0.96505326 4051 0.0057148128 -0.28290855 1.1550208 1.3014361 8496 32 32 0 44803 36480 5329 4051 1.1912109 0 91
|
||||
46000 0.75345782 4064 0.0040245838 -0.30924351 0.81340864 1.7179797 8568 29 29 0 45795 36480 5329 4064 1.1975591 0 91
|
||||
47000 0.87187806 4017 0.004406241 -0.40855293 0.89054538 1.3105257 8586 36 36 0 46822 36480 5329 4017 1.1834816 0 91
|
||||
48000 0.83729235 4078 0.0045115864 -0.33572888 0.91183673 1.3856733 8513 38 38 0 47866 36480 5329 4078 1.1996374 0 91
|
||||
49000 0.65112065 4048 0.0030445536 -0.35483503 0.61533473 1.2659451 8705 32 32 0 48907 36480 5329 4048 1.1907782 0 91
|
||||
50000 0.82730473 4066 0.0045492584 -0.31323342 0.91945063 1.1803982 8562 41 41 0 49965 36480 5329 4066 1.1696702 0 91
|
||||
51000 0.74252279 4048 0.0046741422 -0.16166808 0.94469088 1.5539445 8564 35 35 0 50948 36480 5329 4048 1.1748481 0 91
|
||||
52000 0.85671386 4051 0.0058575179 -0.092640701 1.183863 1.6307333 8609 19 19 0 51894 36480 5329 4051 1.1770671 0 91
|
||||
53000 0.7233951 4068 0.0043421658 -0.20026358 0.87759512 1.453924 8582 28 28 0 52893 36480 5329 4068 1.2027667 0 91
|
||||
54000 0.72117217 4051 0.0040247209 -0.26111018 0.81343635 1.3496518 8679 25 25 0 53831 36480 5329 4051 1.1823115 0 91
|
||||
55000 0.87940919 4044 0.0047057065 -0.35924936 0.95107033 1.240057 8559 34 34 0 54813 36480 5329 4044 1.1815144 0 91
|
||||
56000 0.83192698 4044 0.0046298732 -0.30382753 0.93574367 1.547229 8441 37 37 0 55740 36480 5329 4044 1.1761232 0 91
|
||||
57000 0.91043729 4058 0.0050029377 -0.34540782 1.0111437 1.4951603 8550 32 32 0 56678 36480 5329 4058 1.2024504 0 91
|
||||
58000 0.97648852 4036 0.0053292287 -0.37787747 1.0770904 1.4058278 8554 31 31 0 57683 36480 5329 4036 1.1746239 0 91
|
||||
59000 0.72239185 4018 0.0046615138 -0.1342253 0.94213856 1.8337414 8716 35 35 0 58640 36480 5329 4018 1.1697661 0 91
|
||||
60000 0.73800253 4032 0.0037590001 -0.33989225 0.75973152 1.399426 8561 32 32 0 59593 36480 5329 4032 1.1958194 0 91
|
||||
61000 0.72778603 4060 0.0042599892 -0.22341476 0.86098642 1.3778202 8541 31 31 0 60573 36480 5329 4060 1.1980875 0 91
|
||||
62000 0.80350669 4044 0.0042316822 -0.34195968 0.85526529 1.4379455 8487 37 37 0 61608 36480 5329 4044 1.1942365 0 91
|
||||
63000 0.90084181 4066 0.0043040273 -0.47236734 0.86988695 1.4672845 8504 32 32 0 62670 36480 5329 4066 1.1829834 0 91
|
||||
64000 0.87220486 4059 0.0047840275 -0.33268544 0.9668998 1.5398216 8588 34 34 0 63605 36480 5329 4059 1.1884975 0 91
|
||||
65000 0.82469157 4057 0.004405933 -0.33830733 0.89048312 1.5284565 8783 32 32 0 64693 36480 5329 4057 1.1952722 0 91
|
||||
66000 0.88692288 4081 0.0047264561 -0.36625105 0.95526405 1.3151847 8745 36 36 0 65755 36480 5329 4081 1.1834684 0 91
|
||||
67000 0.83322374 4031 0.0047732147 -0.27678896 0.96471442 1.5085732 8415 34 34 0 66796 36480 5329 4031 1.1969 0 91
|
||||
68000 0.75375865 4020 0.0044379413 -0.22614806 0.89695233 1.6351001 8573 30 30 0 67876 36480 5329 4020 1.1911308 0 91
|
||||
69000 0.91169697 4055 0.0050371842 -0.34036318 1.0180653 1.2495539 8625 20 20 0 68979 36480 5329 4055 1.1860768 0 91
|
||||
70000 0.80502435 4075 0.0042565586 -0.33919322 0.86029306 1.3194042 8571 36 36 0 69947 36480 5329 4075 1.18994 0 91
|
||||
71000 0.8928873 4055 0.0050586026 -0.3080079 1.0223942 1.3949364 8698 32 32 0 71037 36480 5329 4055 1.2154821 0 91
|
||||
72000 0.95397384 4050 0.0052866702 -0.35293209 1.0684889 1.2950893 8613 35 35 0 72090 36480 5329 4050 1.1790804 0 91
|
||||
73000 0.78742879 4053 0.004378612 -0.28830762 0.88496127 1.5168042 8624 30 30 0 73174 36480 5329 4053 1.2008591 0 91
|
||||
74000 0.79498726 4046 0.0042999917 -0.31545969 0.86907133 1.3751647 8562 22 22 0 74250 36480 5329 4046 1.1921334 0 91
|
||||
75000 0.88929145 4051 0.0048995187 -0.33480254 0.99024172 1.6589606 8393 33 33 0 75296 36480 5329 4051 1.1753137 0 91
|
||||
76000 0.98366685 4045 0.0049217494 -0.47092883 0.99473478 1.5271346 8555 29 29 0 76301 36480 5329 4045 1.2031327 0 91
|
||||
77000 0.72618119 4051 0.0035028638 -0.37404618 0.7079638 1.5178344 8565 37 37 0 77315 36480 5329 4051 1.1993308 0 91
|
||||
78000 0.80445682 4028 0.003992176 -0.39178196 0.8068587 1.3682816 8624 32 32 0 78299 36480 5329 4028 1.2065456 0 91
|
||||
79000 1.091703 4052 0.0063793569 -0.33730561 1.2893318 1.5717928 8677 39 39 0 79249 36480 5329 4052 1.1725194 0 91
|
||||
80000 0.77212865 4052 0.0041275152 -0.31625959 0.8342121 1.5583982 8526 33 33 0 80284 36480 5329 4052 1.1981751 0 91
|
||||
81000 0.80732682 4061 0.004618782 -0.26941493 0.93350203 1.5517327 8444 36 36 0 81331 36480 5329 4061 1.2095831 0 91
|
||||
82000 0.80166933 4057 0.0042732734 -0.33081602 0.86367129 1.3937505 8476 29 29 0 82335 36480 5329 4057 1.2047807 0 91
|
||||
83000 0.76980598 4049 0.0041331379 -0.31166241 0.83534851 1.1411979 8561 34 34 0 83375 36480 5329 4049 1.1810941 0 91
|
||||
84000 0.85529188 4076 0.0046148117 -0.34168531 0.93269959 1.3284464 8664 27 27 0 84510 36480 5329 4076 1.192734 0 91
|
||||
85000 0.96167157 4034 0.0053261317 -0.35642617 1.0764645 1.3195071 8557 36 36 0 85517 36480 5329 4034 1.2000123 0 91
|
||||
86000 0.88130862 4047 0.0046646382 -0.37037981 0.94277003 1.3595079 8634 36 36 0 86578 36480 5329 4047 1.1654584 0 91
|
||||
87000 0.68799517 4037 0.0042184867 -0.17251446 0.85259834 1.5087731 8363 40 40 0 87606 36480 5329 4037 1.1833599 0 91
|
||||
88000 0.83191621 4041 0.0048307277 -0.26321678 0.97633838 1.4008912 8597 39 39 0 88490 36480 5329 4041 1.1607031 0 91
|
||||
89000 0.71456519 4036 0.0039378285 -0.26882761 0.79587453 1.2251569 8397 36 36 0 89436 36480 5329 4036 1.1991362 0 91
|
||||
90000 0.75198251 4048 0.0043377839 -0.24374445 0.87670949 1.4896261 8551 29 29 0 90453 36480 5329 4048 1.1899998 0 91
|
||||
91000 0.83310145 4032 0.0049902932 -0.232733 1.0085882 1.4140378 8583 48 48 0 91563 36480 5329 4032 1.1953029 0 91
|
||||
92000 0.8819465 4050 0.0058087956 -0.14008461 1.1740157 1.753218 8610 46 46 0 92618 36480 5329 4050 1.1972268 0 91
|
||||
93000 0.76721608 4048 0.0041923848 -0.29582907 0.8473229 1.4126521 8671 32 32 0 93690 36480 5329 4048 1.2027935 0 91
|
||||
94000 0.8942606 4050 0.0051973822 -0.28200539 1.0504429 1.5743434 8751 21 21 0 94750 36480 5329 4050 1.1804594 0 91
|
||||
95000 0.73609582 4036 0.0035091666 -0.38754512 0.70923765 1.28494 8660 31 31 0 95713 36480 5329 4036 1.1883125 0 91
|
||||
96000 0.79430429 4078 0.0043400156 -0.30635284 0.87716056 1.4351927 8600 38 38 0 96695 36480 5329 4078 1.1704833 0 91
|
||||
97000 0.74817621 4044 0.0038163094 -0.34346826 0.77131429 1.255104 8377 36 36 0 97683 36480 5329 4044 1.1756023 0 91
|
||||
98000 0.78160255 4048 0.0039385343 -0.36857064 0.79601716 1.5320263 8350 25 25 0 98631 36480 5329 4048 1.181196 0 91
|
||||
99000 0.804448 4053 0.004503827 -0.28835905 0.91026848 1.7569548 8506 35 35 0 99687 36480 5329 4053 1.1950898 0 91
|
||||
100000 0.74975993 4032 0.004263269 -0.255493 0.86164929 1.5983872 8621 33 33 0 100701 36480 5329 4032 1.1910217 0 91
|
||||
Loop time of 13.4746 on 8 procs for 100000 steps with 20211 atoms
|
||||
|
||||
Pair time (%) = 0.0563478 (0.418178)
|
||||
Neigh time (%) = 0.794382 (5.89541)
|
||||
Comm time (%) = 1.23773 (9.18569)
|
||||
Outpt time (%) = 0.00554895 (0.0411809)
|
||||
Other time (%) = 11.3806 (84.4595)
|
||||
|
||||
Nlocal: 2526.38 ave 2725 max 2337 min
|
||||
Histogram: 2 0 0 1 1 1 1 0 1 1
|
||||
Nghost: 23.875 ave 27 max 21 min
|
||||
Histogram: 1 1 0 2 0 2 0 0 0 2
|
||||
Neighs: 17 ave 25 max 12 min
|
||||
Histogram: 3 1 0 1 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 136
|
||||
Ave neighs/atom = 0.00672901
|
||||
Neighbor list builds = 5008
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
@ -1,239 +0,0 @@
|
||||
LAMMPS (1 Feb 2014)
|
||||
# SRD viscosity demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
Created orthogonal box = (0 0 -0.912871) to (18.2574 18.2574 0.912871)
|
||||
2 by 4 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big type/fraction 2 0.33 394895
|
||||
35 settings made for type/fraction
|
||||
set group big type/fraction 3 0.5 989894
|
||||
57 settings made for type/fraction
|
||||
group big type 2 3
|
||||
100 atoms in group big
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
100 settings made for mass
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 2.7472 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.16013916 0 1.2654608 1.1298975
|
||||
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
|
||||
Loop time of 0.0173425 on 8 procs for 1000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 0.00033614 (1.93825)
|
||||
Neigh time (%) = 0.000266045 (1.53407)
|
||||
Comm time (%) = 0.0115004 (66.3132)
|
||||
Outpt time (%) = 2.78056e-05 (0.160332)
|
||||
Other time (%) = 0.00521213 (30.0541)
|
||||
|
||||
Nlocal: 12.5 ave 18 max 10 min
|
||||
Histogram: 1 3 1 1 0 1 0 0 0 1
|
||||
Nghost: 27.75 ave 31 max 24 min
|
||||
Histogram: 1 0 1 0 2 2 0 0 0 2
|
||||
Neighs: 19 ave 30 max 16 min
|
||||
Histogram: 4 1 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 152
|
||||
Ave neighs/atom = 1.52
|
||||
Neighbor list builds = 115
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
Lattice spacing in x,y,z = 0.0632456 0.0632456 0.0632456
|
||||
create_atoms 4 region plane
|
||||
Created 83521 atoms
|
||||
|
||||
set type 4 mass 0.1
|
||||
83521 settings made for mass
|
||||
group small type 4
|
||||
83521 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
pair_coeff 2 4 0.0 1.0 1.0
|
||||
pair_coeff 3 4 0.0 1.0 0.75
|
||||
|
||||
delete_atoms overlap 1.0 small big
|
||||
Deleted 63410 atoms, new total = 20211
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.poly.mp
|
||||
|
||||
#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
|
||||
|
||||
run 50000
|
||||
SRD info:
|
||||
SRD/big particles = 20111 100
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 73 73 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250102 0.250102 1.82574
|
||||
SRD per actual grid cell = 4.93717
|
||||
SRD viscosity = 0.23322
|
||||
big/SRD mass density ratio = 0.161311
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.19344 7.74495
|
||||
ave/max big velocity = 1.43991 3.5724
|
||||
Memory usage per processor = 11.8633 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11]
|
||||
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 0.76223471 3964 0.0058318994 0.042955471 1.1786852 3.9611295 7412 29 29 0 611 36480 5329 3964 0.97424113 0 1
|
||||
2000 0.83394503 3951 0.0050432506 -0.22328672 1.0192914 2.7492771 7829 30 30 0 1225 36480 5329 3951 1.0832295 0 3
|
||||
3000 0.86856945 3991 0.0048205728 -0.31988251 0.97428597 2.4105317 7961 34 34 0 2000 36480 5329 3991 1.1243219 0 6
|
||||
4000 0.88106888 4009 0.0066731082 0.035909261 1.3487019 3.025346 8002 33 33 0 2895 36480 5329 4009 1.1359575 0 6
|
||||
5000 1.0764198 4036 0.0070136315 -0.18634051 1.4175251 2.7617336 8117 36 36 0 3808 36480 5329 4036 1.1147743 0 6
|
||||
6000 1.0433139 4004 0.0059532709 -0.35132214 1.2032156 2.3597383 8004 23 23 0 4845 36480 5329 4004 1.1192873 0 6
|
||||
7000 1.1551053 4026 0.0074766715 -0.20999681 1.5111101 2.280806 8269 36 36 0 5873 36480 5329 4026 1.1704244 0 6
|
||||
8000 1.2222713 4008 0.0078175708 -0.24117508 1.5800092 1.967726 8218 33 33 0 7077 36480 5329 4008 1.1496529 0 6
|
||||
9000 1.2240884 4012 0.0081583857 -0.17500037 1.6488913 2.3684675 8502 27 27 0 8359 36480 5329 4012 1.1664455 0 6
|
||||
10000 1.2071315 4035 0.0073838443 -0.30627724 1.4923488 2.124366 8376 33 33 0 9778 36480 5329 4035 1.1942304 0 6
|
||||
11000 1.1694272 4036 0.0077950192 -0.16699527 1.5754513 2.4203067 8623 40 40 0 11210 36480 5329 4036 1.1802896 0 42
|
||||
12000 1.0911561 4044 0.0074117515 -0.12783343 1.4979891 2.4859591 8490 30 30 0 12647 36480 5329 4044 1.171701 0 42
|
||||
13000 1.3535072 4023 0.0091503262 -0.16735325 1.8493724 2.7718999 8320 33 33 0 14082 36480 5329 4023 1.1841757 0 42
|
||||
14000 1.4191753 4043 0.0095368758 -0.18707328 1.927498 2.8442438 8422 25 25 0 15462 36480 5329 4043 1.1567854 0 42
|
||||
15000 1.703769 4053 0.010892787 -0.33707457 2.2015412 2.4160876 8123 34 34 0 16985 36480 5329 4053 1.1875794 0 42
|
||||
16000 1.4270161 4032 0.010142553 -0.076342616 2.0499114 2.9568071 8360 34 34 0 18487 36480 5329 4032 1.164586 0 42
|
||||
17000 1.2267528 4013 0.0080642511 -0.19799584 1.6298658 2.5084784 8477 27 27 0 20101 36480 5329 4013 1.1529604 0 42
|
||||
18000 1.4228586 4050 0.01009573 -0.079611446 2.0404479 2.8013833 8519 33 33 0 21633 36480 5329 4050 1.1549291 0 42
|
||||
19000 1.3041379 4040 0.0082901927 -0.26763462 1.6755308 1.9403854 8483 30 30 0 23194 36480 5329 4040 1.1592747 0 42
|
||||
20000 1.3837406 4030 0.0092446911 -0.19332904 1.8684445 2.4550531 8425 25 25 0 24761 36480 5329 4030 1.1757648 0 42
|
||||
21000 1.7882552 4031 0.012076007 -0.22381856 2.4406817 2.4206092 8581 40 40 0 26371 36480 5329 4031 1.1591574 0 42
|
||||
22000 1.5079803 4015 0.010373742 -0.15025377 2.0966369 2.6321039 8383 33 33 0 27989 36480 5329 4015 1.1495522 0 42
|
||||
23000 1.3835348 4044 0.0087922321 -0.28446888 1.776998 2.2729548 8441 30 30 0 29575 36480 5329 4044 1.1616377 0 42
|
||||
24000 1.5854836 4044 0.0099174248 -0.35795983 2.0044107 2.2250073 8462 35 35 0 31298 36480 5329 4044 1.1796851 0 42
|
||||
25000 1.5314412 4062 0.010880793 -0.082730301 2.1991171 2.6858232 8473 28 28 0 33079 36480 5329 4062 1.1726593 0 54
|
||||
26000 1.2896316 4070 0.0090198232 -0.098554631 1.8229965 2.3437649 8453 40 40 0 34816 36480 5329 4070 1.1764482 0 54
|
||||
27000 1.6956611 4035 0.012064024 -0.088275024 2.43826 2.8138661 8380 32 32 0 36453 36480 5329 4035 1.1622504 0 54
|
||||
28000 1.3560979 4043 0.0088193796 -0.23810107 1.7824848 2.1799536 8611 30 30 0 38202 36480 5329 4043 1.1681248 0 54
|
||||
29000 1.5837646 4029 0.010790526 -0.17893612 2.1808731 2.3116753 8480 26 26 0 39846 36480 5329 4029 1.1774511 0 54
|
||||
30000 1.6549448 4035 0.01137773 -0.16631482 2.2995529 2.6236656 8637 30 30 0 41461 36480 5329 4035 1.1538405 0 54
|
||||
31000 1.445315 4050 0.01013447 -0.1052417 2.0482777 2.4440312 8504 38 38 0 43099 36480 5329 4050 1.1690375 0 54
|
||||
32000 1.5572315 4037 0.010828477 -0.13173155 2.1885434 2.5911192 8453 30 30 0 44760 36480 5329 4037 1.1612147 0 54
|
||||
33000 2.018109 4068 0.013467519 -0.28506208 2.7219203 2.5784978 8701 40 40 0 46462 36480 5329 4068 1.1727186 0 54
|
||||
34000 1.2455134 4066 0.0083640288 -0.16536113 1.6904539 2.3054829 8428 32 32 0 48055 36480 5329 4066 1.1712016 0 54
|
||||
35000 1.6248596 4012 0.011213824 -0.15461501 2.2664259 2.8697537 8453 31 31 0 49658 36480 5329 4012 1.1693962 0 54
|
||||
36000 1.5485873 4039 0.01112737 -0.058442367 2.2489527 3.0386676 8529 42 42 0 51330 36480 5329 4039 1.1750818 0 54
|
||||
37000 1.5561543 4024 0.011313246 -0.032149816 2.2865202 2.7583779 8484 45 45 0 52981 36480 5329 4024 1.1613247 0 54
|
||||
38000 1.5174762 4043 0.010120957 -0.21549294 2.0455467 2.2489655 8528 37 37 0 54637 36480 5329 4043 1.1692017 0 54
|
||||
39000 1.5936544 4045 0.010946409 -0.16216642 2.2123787 2.7579117 8460 35 35 0 56452 36480 5329 4045 1.1670575 0 54
|
||||
40000 1.7884514 4051 0.011913021 -0.2570519 2.4077408 2.494169 8539 37 37 0 58163 36480 5329 4051 1.1744075 0 54
|
||||
41000 1.4173685 4042 0.0096196931 -0.16764288 1.9442362 1.9949409 8511 42 42 0 59967 36480 5329 4042 1.1747318 0 54
|
||||
42000 1.4946304 4055 0.0098254549 -0.24117659 1.9858227 1.9958514 8395 39 39 0 61697 36480 5329 4055 1.1745062 0 54
|
||||
43000 1.6486882 4041 0.011190255 -0.19488288 2.2616625 2.2173122 8473 28 28 0 63447 36480 5329 4041 1.1631975 0 54
|
||||
44000 1.7473914 4055 0.011743128 -0.23020951 2.3734036 2.3913609 8421 30 30 0 65095 36480 5329 4055 1.1567659 0 54
|
||||
45000 1.7826681 4027 0.011993913 -0.23208563 2.4240898 2.4582759 8539 35 35 0 66749 36480 5329 4027 1.1513285 0 54
|
||||
46000 1.3988187 4049 0.0091738733 -0.23010838 1.8541315 2.3866226 8447 38 38 0 68459 36480 5329 4049 1.1728215 0 54
|
||||
47000 1.8402398 4064 0.01271321 -0.17249031 2.569467 2.7748374 8524 33 33 0 70139 36480 5329 4064 1.1555276 0 54
|
||||
48000 1.5634287 4042 0.011047794 -0.096639164 2.2328696 2.7173437 8561 33 33 0 71923 36480 5329 4042 1.177462 0 54
|
||||
49000 1.789207 4058 0.012453079 -0.14902655 2.5168918 2.9310418 8545 38 38 0 73721 36480 5329 4058 1.1581934 0 54
|
||||
50000 1.3475703 4010 0.0092484369 -0.13867816 1.8692016 2.1619389 8664 32 32 0 75439 36480 5329 4010 1.1589691 0 54
|
||||
Loop time of 6.84 on 8 procs for 50000 steps with 20211 atoms
|
||||
|
||||
Pair time (%) = 0.0295508 (0.432029)
|
||||
Neigh time (%) = 0.400359 (5.8532)
|
||||
Comm time (%) = 0.622996 (9.10813)
|
||||
Outpt time (%) = 0.00241029 (0.0352382)
|
||||
Other time (%) = 5.78468 (84.5714)
|
||||
|
||||
Nlocal: 2526.38 ave 2651 max 2342 min
|
||||
Histogram: 1 0 0 2 1 0 0 1 1 2
|
||||
Nghost: 24.5 ave 27 max 23 min
|
||||
Histogram: 1 0 4 0 0 2 0 0 0 1
|
||||
Neighs: 17.375 ave 24 max 13 min
|
||||
Histogram: 2 2 0 1 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 139
|
||||
Ave neighs/atom = 0.00687744
|
||||
Neighbor list builds = 2502
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
317
examples/ASPHERE/poly/log.1Feb24.poly.g++.1
Normal file
317
examples/ASPHERE/poly/log.1Feb24.poly.g++.1
Normal file
@ -0,0 +1,317 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD diffusion demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big type/fraction 2 0.33 394895
|
||||
Setting atom values ...
|
||||
35 settings made for type/fraction
|
||||
set group big type/fraction 3 0.5 989894
|
||||
Setting atom values ...
|
||||
57 settings made for type/fraction
|
||||
group big type 2 3
|
||||
100 atoms in group big
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for mass
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.54
|
||||
ghost atom cutoff = 2.54
|
||||
binsize = 1.27, bins = 15 15 2
|
||||
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/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.16013916 0 1.2654608 1.1298975
|
||||
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
|
||||
Loop time of 0.00622873 on 1 procs for 1000 steps with 100 atoms
|
||||
|
||||
Performance: 69356032.450 tau/day, 160546.371 timesteps/s, 16.055 Matom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0015709 | 0.0015709 | 0.0015709 | 0.0 | 25.22
|
||||
Neigh | 0.0014016 | 0.0014016 | 0.0014016 | 0.0 | 22.50
|
||||
Comm | 0.0012066 | 0.0012066 | 0.0012066 | 0.0 | 19.37
|
||||
Output | 6.169e-06 | 6.169e-06 | 6.169e-06 | 0.0 | 0.10
|
||||
Modify | 0.0013508 | 0.0013508 | 0.0013508 | 0.0 | 21.69
|
||||
Other | | 0.0006926 | | | 11.12
|
||||
|
||||
Nlocal: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 60 ave 60 max 60 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 152 ave 152 max 152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 152
|
||||
Ave neighs/atom = 1.52
|
||||
Neighbor list builds = 115
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
|
||||
create_atoms 4 region plane
|
||||
Created 83521 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
create_atoms CPU = 0.016 seconds
|
||||
|
||||
set type 4 mass 0.1
|
||||
Setting atom values ...
|
||||
83521 settings made for mass
|
||||
group small type 4
|
||||
83521 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
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
|
||||
System init for delete_atoms ...
|
||||
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 14 14 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 63410 atoms, new total = 20211
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.poly
|
||||
|
||||
#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
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 20111 100
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 73 73 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
|
||||
SRD per actual grid cell = 4.9371727
|
||||
SRD viscosity = 0.23321983
|
||||
big/SRD mass density ratio = 0.16131131
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.1934421 7.74495
|
||||
ave/max big velocity = 1.4399093 3.5724039
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.54
|
||||
ghost atom cutoff = 2.54
|
||||
binsize = 18.257419, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 42 | 42 | 42 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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]
|
||||
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.0181191 3924 0.0076572255 0.030604433 1.5476019 3.7992573 7242 26 26 0 635 15876 5329 3924 0.98110339 0 3
|
||||
2000 0.69783736 3992 0.0027817464 -0.47755891 0.56221876 1.9887267 7740 34 34 1 1186 15876 5329 3992 1.0611575 0 24
|
||||
3000 0.89084297 3981 0.004323119 -0.45361044 0.87374558 1.7342893 7775 24 24 0 1923 15876 5329 3981 1.1207371 0 24
|
||||
4000 0.84391846 4036 0.0045581483 -0.33619115 0.92124735 1.8456288 8060 43 43 0 2734 15876 5329 4036 1.1481354 0 24
|
||||
5000 0.69548234 4056 0.0030033315 -0.42926535 0.60700333 1.6113509 8260 33 33 0 3638 15876 5329 4056 1.148749 0 24
|
||||
6000 0.71729125 4023 0.0035318938 -0.35493291 0.71383106 1.673491 8224 29 29 0 4528 15876 5329 4023 1.1602572 0 24
|
||||
7000 0.90145513 4032 0.0047423524 -0.38469129 0.95847685 1.7537778 8382 31 31 0 5395 15876 5329 4032 1.1543513 0 24
|
||||
8000 0.6739295 4026 0.0029910322 -0.39963744 0.60451751 1.646528 8409 35 35 0 6293 15876 5329 4026 1.1540519 0 24
|
||||
9000 0.80563959 4041 0.0042947965 -0.33238166 0.86802133 1.6597032 8429 29 29 0 7164 15876 5329 4041 1.1880521 0 24
|
||||
10000 0.90407954 4022 0.0046865656 -0.39987673 0.94720178 1.445708 8349 30 30 0 8189 15876 5329 4022 1.171667 0 24
|
||||
Loop time of 5.64963 on 1 procs for 10000 steps with 20211 atoms
|
||||
|
||||
Performance: 152930.340 tau/day, 1770.027 timesteps/s, 35.774 Matom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.019832 | 0.019832 | 0.019832 | 0.0 | 0.35
|
||||
Neigh | 0.020738 | 0.020738 | 0.020738 | 0.0 | 0.37
|
||||
Comm | 0.056875 | 0.056875 | 0.056875 | 0.0 | 1.01
|
||||
Output | 0.00083247 | 0.00083247 | 0.00083247 | 0.0 | 0.01
|
||||
Modify | 5.4828 | 5.4828 | 5.4828 | 0.0 | 97.05
|
||||
Other | | 0.06854 | | | 1.21
|
||||
|
||||
Nlocal: 20211 ave 20211 max 20211 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 49 ave 49 max 49 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 160 ave 160 max 160 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 160
|
||||
Ave neighs/atom = 0.0079164811
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:11
|
||||
317
examples/ASPHERE/poly/log.1Feb24.poly.g++.4
Normal file
317
examples/ASPHERE/poly/log.1Feb24.poly.g++.4
Normal file
@ -0,0 +1,317 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD diffusion demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big type/fraction 2 0.33 394895
|
||||
Setting atom values ...
|
||||
35 settings made for type/fraction
|
||||
set group big type/fraction 3 0.5 989894
|
||||
Setting atom values ...
|
||||
57 settings made for type/fraction
|
||||
group big type 2 3
|
||||
100 atoms in group big
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for mass
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.54
|
||||
ghost atom cutoff = 2.54
|
||||
binsize = 1.27, bins = 15 15 2
|
||||
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/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.16013916 0 1.2654608 1.1298975
|
||||
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
|
||||
Loop time of 0.00891987 on 4 procs for 1000 steps with 100 atoms
|
||||
|
||||
Performance: 48431181.463 tau/day, 112109.216 timesteps/s, 11.211 Matom-step/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00039835 | 0.00043547 | 0.00047558 | 0.0 | 4.88
|
||||
Neigh | 0.00033856 | 0.00036829 | 0.00038548 | 0.0 | 4.13
|
||||
Comm | 0.0065535 | 0.0065882 | 0.0066353 | 0.0 | 73.86
|
||||
Output | 1.0991e-05 | 1.2359e-05 | 1.4677e-05 | 0.0 | 0.14
|
||||
Modify | 0.00043639 | 0.00045662 | 0.00050811 | 0.0 | 5.12
|
||||
Other | | 0.001059 | | | 11.87
|
||||
|
||||
Nlocal: 25 ave 29 max 23 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 33.75 ave 35 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
Neighs: 38 ave 46 max 34 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 152
|
||||
Ave neighs/atom = 1.52
|
||||
Neighbor list builds = 115
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
|
||||
create_atoms 4 region plane
|
||||
Created 83521 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
create_atoms CPU = 0.006 seconds
|
||||
|
||||
set type 4 mass 0.1
|
||||
Setting atom values ...
|
||||
83521 settings made for mass
|
||||
group small type 4
|
||||
83521 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
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
|
||||
System init for delete_atoms ...
|
||||
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 14 14 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 63410 atoms, new total = 20211
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.poly
|
||||
|
||||
#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
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 20111 100
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 73 73 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
|
||||
SRD per actual grid cell = 4.9371727
|
||||
SRD viscosity = 0.23321983
|
||||
big/SRD mass density ratio = 0.16131131
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.1934421 7.74495
|
||||
ave/max big velocity = 1.4399093 3.5724039
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.54
|
||||
ghost atom cutoff = 2.54
|
||||
binsize = 18.257419, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.17 | 19.17 | 19.18 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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]
|
||||
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 0.98459665 3968 0.0086216557 0.27547381 1.7425228 4.4010488 7403 34 34 0 663 25600 5329 3968 0.98292304 0 5
|
||||
2000 0.74381104 4003 0.0041077507 -0.27806095 0.8302175 2.6170187 7746 32 32 0 1272 25600 5329 4003 1.0631936 0 5
|
||||
3000 0.86305095 3969 0.0048953507 -0.29654658 0.98939933 2.1215334 7834 35 35 0 1974 25600 5329 3969 1.1209619 0 5
|
||||
4000 0.8262932 4022 0.0049907905 -0.2224882 1.0086887 2.079935 8196 27 27 0 2753 25600 5329 4022 1.1040604 0 5
|
||||
5000 0.85908819 4038 0.0043301633 -0.40487209 0.87516931 1.7917343 8347 28 28 0 3622 25600 5329 4038 1.1575336 0 5
|
||||
6000 0.8048766 4024 0.0047529981 -0.2386377 0.96062844 1.8195477 8103 26 26 0 4536 25600 5329 4024 1.1818796 0 5
|
||||
7000 0.84561126 4047 0.0039459142 -0.46245206 0.79750871 1.4432235 8154 20 20 0 5483 25600 5329 4047 1.1817402 0 5
|
||||
8000 0.81543891 4037 0.0037591562 -0.45524091 0.75976306 1.7501338 8377 27 27 0 6472 25600 5329 4037 1.168956 0 5
|
||||
9000 0.71960112 4045 0.0035243955 -0.3598901 0.71231557 1.7333111 8440 30 30 0 7386 25600 5329 4045 1.1765277 0 5
|
||||
10000 1.0831334 4043 0.0053045911 -0.54175788 1.0721109 1.7434822 8283 33 33 0 8331 25600 5329 4043 1.1696048 0 5
|
||||
Loop time of 1.82855 on 4 procs for 10000 steps with 20211 atoms
|
||||
|
||||
Performance: 472504.837 tau/day, 5468.806 timesteps/s, 110.530 Matom-step/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 | 0.0057481 | 0.0069625 | 0.0087051 | 1.3 | 0.38
|
||||
Neigh | 0.0067658 | 0.0070766 | 0.0076303 | 0.4 | 0.39
|
||||
Comm | 0.10613 | 0.10693 | 0.10786 | 0.2 | 5.85
|
||||
Output | 0.00053606 | 0.00059075 | 0.00063891 | 0.0 | 0.03
|
||||
Modify | 1.6117 | 1.6525 | 1.6763 | 1.9 | 90.37
|
||||
Other | | 0.05449 | | | 2.98
|
||||
|
||||
Nlocal: 5052.75 ave 5483 max 4509 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 27 ave 28 max 26 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 39.5 ave 55 max 26 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 158
|
||||
Ave neighs/atom = 0.0078175251
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
318
examples/ASPHERE/poly/log.1Feb24.poly.mp.g++.1
Normal file
318
examples/ASPHERE/poly/log.1Feb24.poly.mp.g++.1
Normal file
@ -0,0 +1,318 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD viscosity demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big type/fraction 2 0.33 394895
|
||||
Setting atom values ...
|
||||
35 settings made for type/fraction
|
||||
set group big type/fraction 3 0.5 989894
|
||||
Setting atom values ...
|
||||
57 settings made for type/fraction
|
||||
group big type 2 3
|
||||
100 atoms in group big
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for mass
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.54
|
||||
ghost atom cutoff = 2.54
|
||||
binsize = 1.27, bins = 15 15 2
|
||||
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/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.16013916 0 1.2654608 1.1298975
|
||||
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
|
||||
Loop time of 0.00627198 on 1 procs for 1000 steps with 100 atoms
|
||||
|
||||
Performance: 68877814.583 tau/day, 159439.386 timesteps/s, 15.944 Matom-step/s
|
||||
97.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0016224 | 0.0016224 | 0.0016224 | 0.0 | 25.87
|
||||
Neigh | 0.0014238 | 0.0014238 | 0.0014238 | 0.0 | 22.70
|
||||
Comm | 0.0011671 | 0.0011671 | 0.0011671 | 0.0 | 18.61
|
||||
Output | 6.058e-06 | 6.058e-06 | 6.058e-06 | 0.0 | 0.10
|
||||
Modify | 0.0013659 | 0.0013659 | 0.0013659 | 0.0 | 21.78
|
||||
Other | | 0.0006868 | | | 10.95
|
||||
|
||||
Nlocal: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 60 ave 60 max 60 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 152 ave 152 max 152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 152
|
||||
Ave neighs/atom = 1.52
|
||||
Neighbor list builds = 115
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
|
||||
create_atoms 4 region plane
|
||||
Created 83521 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
create_atoms CPU = 0.017 seconds
|
||||
|
||||
set type 4 mass 0.1
|
||||
Setting atom values ...
|
||||
83521 settings made for mass
|
||||
group small type 4
|
||||
83521 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
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
|
||||
System init for delete_atoms ...
|
||||
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 14 14 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 63410 atoms, new total = 20211
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.poly.mp
|
||||
|
||||
#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
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 20111 100
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 73 73 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
|
||||
SRD per actual grid cell = 4.9371727
|
||||
SRD viscosity = 0.23321983
|
||||
big/SRD mass density ratio = 0.16131131
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.1934421 7.74495
|
||||
ave/max big velocity = 1.4399093 3.5724039
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.54
|
||||
ghost atom cutoff = 2.54
|
||||
binsize = 18.257419, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 42 | 42 | 42 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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]
|
||||
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 0.9260989 3936 0.007125623 0.060272296 1.4401597 3.9323 7454 34 34 0 666 15876 5329 3936 0.98459206 0 28
|
||||
2000 0.90353395 4000 0.0052889652 -0.27731283 1.0689528 2.6405627 7698 23 23 0 1382 15876 5329 4000 1.0797162 0 46
|
||||
3000 0.90859187 3993 0.0052873224 -0.28518115 1.0686207 2.2965966 7968 31 31 0 2142 15876 5329 3993 1.1267833 0 46
|
||||
4000 0.84755099 4048 0.005174979 -0.21693597 1.045915 2.3794577 8137 36 36 0 3087 15876 5329 4048 1.1357649 0 46
|
||||
5000 0.970415 4034 0.0070498808 -0.021066942 1.4248514 2.7424457 8202 29 29 0 4119 15876 5329 4034 1.1354594 0 46
|
||||
6000 1.3230208 4023 0.0094580142 -0.059741745 1.9115593 3.1405056 8259 36 36 0 5151 15876 5329 4023 1.1508111 0 46
|
||||
7000 1.2356555 4022 0.0076141503 -0.30223075 1.5388959 2.2740088 8336 33 33 0 6277 15876 5329 4022 1.1814599 0 46
|
||||
8000 1.0470467 4044 0.0077098735 -0.001857114 1.5582425 2.97413 8285 40 40 0 7399 15876 5329 4044 1.1644871 0 46
|
||||
9000 1.0827168 4054 0.0062150407 -0.35712609 1.2561219 2.0991523 8454 31 31 0 8664 15876 5329 4054 1.1744383 0 46
|
||||
10000 1.3953419 4031 0.0091083246 -0.23817595 1.8408835 2.4493963 8468 34 34 0 10227 15876 5329 4031 1.1657737 0 62
|
||||
Loop time of 5.74914 on 1 procs for 10000 steps with 20211 atoms
|
||||
|
||||
Performance: 150283.390 tau/day, 1739.391 timesteps/s, 35.155 Matom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.021224 | 0.021224 | 0.021224 | 0.0 | 0.37
|
||||
Neigh | 0.020586 | 0.020586 | 0.020586 | 0.0 | 0.36
|
||||
Comm | 0.057881 | 0.057881 | 0.057881 | 0.0 | 1.01
|
||||
Output | 0.00093386 | 0.00093386 | 0.00093386 | 0.0 | 0.02
|
||||
Modify | 5.579 | 5.579 | 5.579 | 0.0 | 97.04
|
||||
Other | | 0.06951 | | | 1.21
|
||||
|
||||
Nlocal: 20211 ave 20211 max 20211 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 50 ave 50 max 50 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 141 ave 141 max 141 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 141
|
||||
Ave neighs/atom = 0.006976399
|
||||
Neighbor list builds = 503
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:11
|
||||
318
examples/ASPHERE/poly/log.1Feb24.poly.mp.g++.4
Normal file
318
examples/ASPHERE/poly/log.1Feb24.poly.mp.g++.4
Normal file
@ -0,0 +1,318 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD viscosity demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big type/fraction 2 0.33 394895
|
||||
Setting atom values ...
|
||||
35 settings made for type/fraction
|
||||
set group big type/fraction 3 0.5 989894
|
||||
Setting atom values ...
|
||||
57 settings made for type/fraction
|
||||
group big type 2 3
|
||||
100 atoms in group big
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
Setting atom values ...
|
||||
100 settings made for mass
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.54
|
||||
ghost atom cutoff = 2.54
|
||||
binsize = 1.27, bins = 15 15 2
|
||||
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/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.16013916 0 1.2654608 1.1298975
|
||||
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
|
||||
Loop time of 0.00883083 on 4 procs for 1000 steps with 100 atoms
|
||||
|
||||
Performance: 48919544.759 tau/day, 113239.687 timesteps/s, 11.324 Matom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00040021 | 0.00044336 | 0.00050371 | 0.0 | 5.02
|
||||
Neigh | 0.00033682 | 0.00036617 | 0.00038566 | 0.0 | 4.15
|
||||
Comm | 0.006519 | 0.0065578 | 0.0066015 | 0.0 | 74.26
|
||||
Output | 1.1215e-05 | 1.2252e-05 | 1.4089e-05 | 0.0 | 0.14
|
||||
Modify | 0.00043326 | 0.00044482 | 0.00046058 | 0.0 | 5.04
|
||||
Other | | 0.001006 | | | 11.40
|
||||
|
||||
Nlocal: 25 ave 29 max 23 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 33.75 ave 35 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
Neighs: 38 ave 46 max 34 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 152
|
||||
Ave neighs/atom = 1.52
|
||||
Neighbor list builds = 115
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553
|
||||
create_atoms 4 region plane
|
||||
Created 83521 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093)
|
||||
create_atoms CPU = 0.006 seconds
|
||||
|
||||
set type 4 mass 0.1
|
||||
Setting atom values ...
|
||||
83521 settings made for mass
|
||||
group small type 4
|
||||
83521 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
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
|
||||
System init for delete_atoms ...
|
||||
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 14 14 2
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 63410 atoms, new total = 20211
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.poly.mp
|
||||
|
||||
#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
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 20111 100
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 73 73 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419
|
||||
SRD per actual grid cell = 4.9371727
|
||||
SRD viscosity = 0.23321983
|
||||
big/SRD mass density ratio = 0.16131131
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.1934421 7.74495
|
||||
ave/max big velocity = 1.4399093 3.5724039
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.54
|
||||
ghost atom cutoff = 2.54
|
||||
binsize = 18.257419, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.17 | 19.17 | 19.18 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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]
|
||||
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 0.83735494 3964 0.0071370659 0.19481352 1.4424724 3.9770741 7472 25 25 0 603 25600 5329 3964 0.96475118 0 2
|
||||
2000 0.89694821 3981 0.0057098818 -0.18242861 1.1540242 3.1251883 7672 28 28 0 1238 25600 5329 3981 1.0589985 0 2
|
||||
3000 0.99778172 3975 0.0051822049 -0.43931933 1.0473754 1.8970896 7814 24 24 0 1968 25600 5329 3975 1.1192504 0 3
|
||||
4000 0.90067439 4030 0.0045096255 -0.43056442 0.91144042 1.8769981 8104 33 33 0 2911 25600 5329 4030 1.1382082 0 3
|
||||
5000 0.90625848 4018 0.0055622776 -0.22613322 1.1241919 2.1866405 8287 26 26 0 3900 25600 5329 4018 1.1429442 0 3
|
||||
6000 1.1284139 4022 0.0065653291 -0.354418 1.3269187 2.0312152 8268 35 35 0 5013 25600 5329 4022 1.1559733 0 3
|
||||
7000 1.0073477 4043 0.0063924548 -0.2089691 1.291979 2.3332058 8433 39 39 0 6093 25600 5329 4043 1.1308958 0 3
|
||||
8000 1.0621801 4050 0.00731979 -0.10324558 1.4794028 2.6610716 8353 40 40 0 7194 25600 5329 4050 1.1539521 0 3
|
||||
9000 1.3173319 4046 0.0085268497 -0.23946297 1.7233616 2.4074596 8290 33 33 0 8498 25600 5329 4046 1.1601502 0 3
|
||||
10000 1.1754738 4009 0.0074264713 -0.25049186 1.5009641 2.4237351 8305 30 30 0 9811 25600 5329 4009 1.1489476 0 43
|
||||
Loop time of 1.85719 on 4 procs for 10000 steps with 20211 atoms
|
||||
|
||||
Performance: 465218.852 tau/day, 5384.477 timesteps/s, 108.826 Matom-step/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 | 0.0056791 | 0.0069765 | 0.0089852 | 1.6 | 0.38
|
||||
Neigh | 0.006991 | 0.0073805 | 0.0079507 | 0.4 | 0.40
|
||||
Comm | 0.10756 | 0.10836 | 0.10942 | 0.2 | 5.83
|
||||
Output | 0.00052479 | 0.0005511 | 0.00062567 | 0.0 | 0.03
|
||||
Modify | 1.6443 | 1.6772 | 1.7031 | 1.7 | 90.31
|
||||
Other | | 0.0567 | | | 3.05
|
||||
|
||||
Nlocal: 5052.75 ave 5381 max 4651 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nghost: 28.5 ave 30 max 26 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Neighs: 34.75 ave 55 max 26 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 139
|
||||
Ave neighs/atom = 0.006877443
|
||||
Neighbor list builds = 501
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -1,111 +1,111 @@
|
||||
# SRD diffusion demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
compute tbig all temp/sphere
|
||||
thermo_modify temp tbig
|
||||
compute tbig all temp/sphere
|
||||
thermo_modify temp tbig
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
delete_atoms overlap 0.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
uncompute tbig
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star
|
||||
#dump 1 all atom 1000 dump.star
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
run 10000
|
||||
|
||||
@ -1,112 +1,112 @@
|
||||
# SRD viscosity demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
compute tbig all temp/sphere
|
||||
thermo_modify temp tbig
|
||||
compute tbig all temp/sphere
|
||||
thermo_modify temp tbig
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
delete_atoms overlap 0.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
uncompute tbig
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star.mp
|
||||
#dump 1 all atom 1000 dump.star.mp
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
run 10000
|
||||
|
||||
@ -1,290 +0,0 @@
|
||||
LAMMPS (1 Feb 2014)
|
||||
# SRD diffusion demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
orthogonal box = (-13.2934 -13.2934 -0.5) to (13.2934 13.2934 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
270 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
270 settings made for mass
|
||||
group big type 1
|
||||
270 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 2.64859 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0.24721146
|
||||
100 0 3.291475 0 3.291475 0.69158089
|
||||
200 0 4.6176595 0 4.6176595 0.71737945
|
||||
300 0 7.0921814 0 7.0921814 1.2163497
|
||||
400 0 8.3666709 0 8.3666709 0.50645957
|
||||
500 0 10.630838 0 10.630838 0.72764487
|
||||
600 0 12.42157 0 12.42157 1.0130599
|
||||
700 0 14.349074 0 14.349074 0.74795509
|
||||
800 0 16.464746 0 16.464746 1.054549
|
||||
900 0 18.253108 0 18.253108 0.51551753
|
||||
1000 0 20.699563 0 20.699563 1.8084662
|
||||
Loop time of 0.040709 on 8 procs for 1000 steps with 270 atoms
|
||||
|
||||
Pair time (%) = 0.00249004 (6.11668)
|
||||
Neigh time (%) = 0.000995547 (2.44552)
|
||||
Comm time (%) = 0.0116902 (28.7165)
|
||||
Outpt time (%) = 0.000232756 (0.571755)
|
||||
Other time (%) = 0.0253005 (62.1496)
|
||||
|
||||
Nlocal: 33.75 ave 42 max 22 min
|
||||
Histogram: 1 0 1 0 0 2 0 1 1 2
|
||||
Nghost: 23.375 ave 30 max 14 min
|
||||
Histogram: 1 0 1 0 0 2 1 0 1 2
|
||||
Neighs: 52.25 ave 69 max 27 min
|
||||
Histogram: 1 0 1 0 1 0 1 1 1 2
|
||||
|
||||
Total # of neighbors = 418
|
||||
Ave neighs/atom = 1.54815
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 60025 atoms
|
||||
|
||||
set type 2 mass 0.1
|
||||
60025 settings made for mass
|
||||
group small type 2
|
||||
60025 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
Deleted 16305 atoms, new total = 43990
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 43720 270
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 106 106 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250819 0.250819 1
|
||||
SRD per actual grid cell = 5.55866
|
||||
SRD viscosity = 0.235582
|
||||
big/SRD mass density ratio = 0.144099
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.19085 7.72582
|
||||
ave/max big velocity = 2.20262 5.4168
|
||||
Memory usage per processor = 7.83759 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.3155168 8201 0.22979575 37.225304 37.439685 8.9588433 14577 56 56 0 687 57680 11236 8201 1.0283377 0 5 0
|
||||
2000 0.82290815 8187 0.22918912 37.206746 37.340849 6.0607727 14326 56 56 0 1524 57680 11236 8187 1.0127464 0 5 0
|
||||
3000 0.99928391 8168 0.22921842 37.182777 37.345623 10.268998 14389 68 68 0 2274 57680 11236 8168 1.023497 0 5 0
|
||||
4000 1.0348458 8200 0.22920437 37.174693 37.343335 9.8954805 14335 51 51 0 3047 57680 11236 8200 1.0156984 0 5 0
|
||||
5000 1.1496765 8199 0.22939095 37.186379 37.373733 8.0143223 14444 74 74 0 3868 57680 11236 8199 1.0104858 0 5 0
|
||||
6000 0.91767381 8225 0.2292466 37.200668 37.350215 8.6189298 14131 61 61 0 4594 57680 11236 8225 1.0147272 0 5 0
|
||||
7000 0.74806752 8203 0.22888634 37.169611 37.291518 9.8613421 14121 53 53 1 5322 57680 11236 8203 1.0198289 0 19 0
|
||||
8000 1.1177867 8213 0.22924801 37.168286 37.350444 7.911691 14380 62 62 0 6024 57680 11236 8213 1.0066799 0 19 0
|
||||
9000 1.1258411 8209 0.22939703 37.191253 37.374723 6.7377179 14350 51 51 0 6821 57680 11236 8209 1.0081225 0 19 0
|
||||
10000 1.0597344 8182 0.22919436 37.169006 37.341703 9.7769156 14372 48 48 0 7543 57680 11236 8182 1.0099373 0 19 0
|
||||
11000 1.3337199 8159 0.22943046 37.162823 37.38017 6.0897666 14359 58 58 0 8245 57680 11236 8159 1.0046221 0 19 0
|
||||
12000 1.0280975 8184 0.22894286 37.133186 37.300728 2.555317 14162 51 51 0 8935 57680 11236 8184 1.0010306 0 19 0
|
||||
13000 1.2318533 8190 0.22921487 37.144299 37.345045 6.1739989 14285 64 64 0 9634 57680 11236 8190 1.0138112 0 19 0
|
||||
14000 1.1851991 8215 0.22915708 37.142485 37.335629 7.8380175 14151 66 66 0 10407 57680 11236 8215 1.0008011 0 19 0
|
||||
15000 0.89853218 8214 0.22897294 37.159201 37.305628 4.0743953 14077 61 61 0 11069 57680 11236 8214 1.0041341 0 19 0
|
||||
16000 1.0295974 8176 0.22891205 37.127921 37.295708 8.7527117 14000 48 48 0 11832 57680 11236 8176 1.0089653 0 23 0
|
||||
17000 1.1793664 8219 0.22906268 37.128056 37.320249 5.2583304 14268 57 57 0 12490 57680 11236 8219 1.0157079 0 23 0
|
||||
18000 0.90486919 8180 0.22891008 37.147927 37.295387 4.8498125 13939 64 64 0 13154 57680 11236 8180 0.99700921 0 23 0
|
||||
19000 0.81486319 8219 0.22881911 37.147773 37.280566 1.6338041 13934 59 59 1 13861 57680 11236 8219 1.0099189 0 23 0
|
||||
20000 1.0146287 8180 0.22896254 37.138587 37.303934 2.1682593 14057 45 45 0 14593 57680 11236 8180 1.0009466 0 23 0
|
||||
21000 1.3031463 8164 0.22920646 37.131309 37.343674 6.570906 13944 65 65 0 15323 57680 11236 8164 0.98955239 0 23 0
|
||||
22000 1.1258162 8174 0.22915084 37.151147 37.334613 9.0817519 14052 56 56 0 16042 57680 11236 8174 1.0083228 0 23 0
|
||||
23000 1.1421222 8217 0.22906722 37.134865 37.320989 8.0529401 14143 66 66 0 16797 57680 11236 8217 1.0111161 0 23 0
|
||||
24000 0.77402445 8168 0.22883056 37.156294 37.282431 6.8609899 14258 62 62 0 17559 57680 11236 8168 1.0080535 0 23 0
|
||||
25000 0.94006632 8215 0.22879533 37.123496 37.276692 3.8570839 14446 48 48 0 18267 57680 11236 8215 1.0087899 0 23 0
|
||||
26000 1.2808563 8192 0.22933112 37.155253 37.363985 5.3591484 13960 54 54 1 19004 57680 11236 8192 1.0101851 0 79 0
|
||||
27000 1.0266075 8171 0.22898652 37.140542 37.307841 2.9961422 14049 56 56 1 19683 57680 11236 8171 0.99950217 0 79 0
|
||||
28000 0.98185838 8199 0.22867129 37.096475 37.256481 12.080529 14106 61 62 0 20417 57680 11236 8199 1.0026548 0 79 0
|
||||
29000 0.96921352 8192 0.22861802 37.089856 37.247802 8.257635 13891 63 64 0 21169 57680 11236 8192 1.0128041 0 79 0
|
||||
30000 1.0107665 8223 0.22866616 37.090929 37.255646 9.4280788 14021 61 61 1 21863 57680 11236 8223 1.0034994 0 79 0
|
||||
31000 1.1859435 8195 0.22877222 37.079661 37.272926 7.3863353 14093 78 78 0 22480 57680 11236 8195 0.9945582 0 79 0
|
||||
32000 1.2951374 8172 0.22897044 37.094161 37.30522 6.4322363 13792 52 52 0 23151 57680 11236 8172 1.0026092 0 79 0
|
||||
33000 0.82899919 8176 0.22823894 37.050944 37.186041 0.60210493 13797 62 62 0 23903 57680 11236 8176 1.0051075 0 79 0
|
||||
34000 0.96685714 8165 0.22828901 37.036637 37.194199 8.1409866 13837 50 50 0 24591 57680 11236 8165 1.0157895 0 79 0
|
||||
35000 0.95645753 8206 0.22833008 37.045022 37.200889 8.9956195 14130 63 63 0 25340 57680 11236 8206 1.0030424 0 79 0
|
||||
36000 1.2933379 8197 0.22879201 37.065383 37.27615 8.3938627 13978 80 80 0 26085 57680 11236 8197 1.0094497 0 79 0
|
||||
37000 1.1511434 8176 0.22861016 37.058929 37.246523 4.9481995 13856 49 49 1 26759 57680 11236 8176 1.0063722 0 79 0
|
||||
38000 0.93310274 8181 0.22837532 37.056199 37.20826 5.9575015 13949 51 51 0 27445 57680 11236 8181 1.0152607 0 79 0
|
||||
39000 1.0352467 8215 0.22861437 37.078501 37.247208 9.8519532 14109 69 69 0 28245 57680 11236 8215 1.005523 0 79 0
|
||||
40000 1.2696427 8193 0.22885162 37.078957 37.285862 8.4680587 13931 54 55 0 28960 57680 11236 8193 1.0014074 0 79 0
|
||||
41000 1.3270531 8193 0.22909573 37.109374 37.325634 4.3731598 14115 62 62 0 29668 57680 11236 8193 1.0022493 0 79 0
|
||||
42000 1.3650738 8183 0.22911257 37.105921 37.328377 6.6345101 13659 52 52 0 30400 57680 11236 8183 1.0145834 0 79 0
|
||||
43000 1.0780084 8209 0.22855316 37.06156 37.237235 5.5147087 14062 52 52 0 31092 57680 11236 8209 1.0031365 0 79 0
|
||||
44000 0.96146724 8193 0.22846546 37.066263 37.222946 9.7967735 13699 56 56 0 31771 57680 11236 8193 1.0072364 0 79 0
|
||||
45000 1.1733618 8200 0.2286481 37.061489 37.252703 9.8058881 13967 51 52 0 32532 57680 11236 8200 1.0068663 0 79 0
|
||||
46000 0.94784989 8211 0.22845052 37.066048 37.220513 5.8834756 13944 34 35 0 33213 57680 11236 8211 1.0080225 0 79 0
|
||||
47000 1.2354771 8207 0.22859598 37.042876 37.244213 6.1458407 13851 56 56 0 33886 57680 11236 8207 1.0151781 0 79 0
|
||||
48000 1.0834097 8164 0.22835968 37.029157 37.205712 6.7378814 13944 56 56 0 34578 57680 11236 8164 1.0128575 0 79 0
|
||||
49000 0.9386786 8208 0.22837254 37.054838 37.207808 5.0809383 13618 53 53 0 35328 57680 11236 8208 1.0045622 0 79 0
|
||||
50000 1.047176 8154 0.22859126 37.072791 37.243442 4.8016981 13847 55 55 0 36059 57680 11236 8154 1.0005378 0 79 0
|
||||
51000 1.0943417 8222 0.22844191 37.040773 37.21911 7.9359541 13897 61 61 0 36711 57680 11236 8222 1.0036343 0 79 0
|
||||
52000 1.2811259 8200 0.22871149 37.054255 37.263031 4.9958687 13744 56 56 0 37402 57680 11236 8200 1.0049188 0 79 0
|
||||
53000 1.0997162 8218 0.22853173 37.05453 37.233743 4.6772882 13967 65 65 0 38082 57680 11236 8218 1.0054533 0 79 0
|
||||
54000 0.97625718 8185 0.2283994 37.05309 37.212184 5.9026406 13741 69 69 0 38761 57680 11236 8185 0.99393606 0 79 0
|
||||
55000 0.97919465 8192 0.22835234 37.044944 37.204516 6.8419755 13990 58 58 0 39453 57680 11236 8192 1.0103052 0 79 0
|
||||
56000 0.86300824 8181 0.22842164 37.075169 37.215808 6.8288348 13751 57 57 0 40118 57680 11236 8181 0.99683099 0 79 0
|
||||
57000 0.89429559 8181 0.22851743 37.085677 37.231414 9.378853 13746 72 72 0 40730 57680 11236 8181 1.0086882 0 79 0
|
||||
58000 1.0853441 8172 0.22857719 37.064279 37.24115 7.4580035 13869 58 58 1 41462 57680 11236 8172 1.0092141 0 79 0
|
||||
59000 1.0149632 8199 0.22868187 37.092803 37.258205 8.2913359 13720 54 54 0 42159 57680 11236 8199 1.0082738 0 79 0
|
||||
60000 0.99214038 8241 0.22871146 37.101344 37.263026 7.9905647 13776 67 67 0 42858 57680 11236 8241 1.0027929 0 79 0
|
||||
61000 0.95721926 8211 0.2285241 37.07651 37.232501 11.837258 13907 62 62 0 43565 57680 11236 8211 1.0201117 0 79 0
|
||||
62000 1.1457294 8195 0.22866514 37.068769 37.25548 9.7934944 13796 40 40 1 44292 57680 11236 8195 1.005192 0 79 0
|
||||
63000 1.1096177 8193 0.22863037 37.068989 37.249815 8.0809047 13984 54 55 0 44986 57680 11236 8193 1.0076438 0 79 0
|
||||
64000 1.1643495 8168 0.22860016 37.055147 37.244893 4.7376475 13857 50 50 1 45657 57680 11236 8168 1.002011 0 79 0
|
||||
65000 1.2172585 8201 0.22845803 37.023368 37.221736 8.9744616 13610 53 53 0 46295 57680 11236 8201 1.0033999 0 79 0
|
||||
66000 0.99924611 8189 0.22807344 36.996237 37.159077 8.5854786 13849 49 49 0 46944 57680 11236 8189 1.015528 0 79 0
|
||||
67000 1.2543542 8165 0.22831075 36.993327 37.19774 5.0081411 13906 57 58 1 47666 57680 11236 8165 1.0189753 0 79 0
|
||||
68000 1.0360874 8205 0.22812149 36.99806 37.166904 2.2431831 13650 52 52 0 48363 57680 11236 8205 1.0076864 0 79 0
|
||||
69000 0.69755552 8218 0.22766249 36.978446 37.092121 4.2769033 13654 51 51 0 49044 57680 11236 8218 1.009863 0 79 0
|
||||
70000 0.90921994 8167 0.22796236 36.992809 37.140978 9.3555738 13927 52 52 0 49793 57680 11236 8167 1.0015807 0 79 0
|
||||
71000 0.95608837 8177 0.22797832 36.987772 37.143579 8.0740708 13612 63 63 0 50464 57680 11236 8177 1.0097491 0 79 0
|
||||
72000 1.0374855 8192 0.22803745 36.98414 37.153212 4.4789755 13561 52 52 0 51127 57680 11236 8192 0.99496724 0 79 0
|
||||
73000 0.90636338 8214 0.22783374 36.97232 37.120024 9.3364171 13598 53 53 0 51799 57680 11236 8214 1.0078219 0 79 0
|
||||
74000 1.1869638 8179 0.22834625 37.010094 37.203525 4.8292929 13771 51 51 0 52500 57680 11236 8179 0.98865277 0 79 0
|
||||
75000 1.0177351 8188 0.22826506 37.024443 37.190296 5.1808505 13508 55 55 0 53183 57680 11236 8188 0.99903558 0 79 0
|
||||
76000 1.062496 8230 0.22820987 37.008158 37.181305 8.1032524 13769 58 58 0 53864 57680 11236 8230 0.99397021 0 79 0
|
||||
77000 0.9762027 8131 0.22831271 37.038975 37.19806 10.309798 13787 47 47 0 54553 57680 11236 8131 1.0066289 0 79 0
|
||||
78000 1.0688533 8160 0.22855677 37.06364 37.237824 7.4800503 13224 58 58 0 55248 57680 11236 8160 1.0073477 0 79 0
|
||||
79000 1.2598513 8151 0.22844942 37.015024 37.220333 7.4724924 13859 63 63 0 55911 57680 11236 8151 1.0065168 0 79 0
|
||||
80000 1.1044575 8176 0.22834306 37.023019 37.203005 3.0142586 13579 62 62 0 56611 57680 11236 8176 1.0008704 0 79 0
|
||||
81000 1.2756491 8205 0.22853748 37.026797 37.23468 6.434309 13702 52 52 0 57313 57680 11236 8205 1.0058366 0 79 0
|
||||
82000 1.1276926 8193 0.22857049 37.056287 37.240059 11.825248 13621 63 63 0 58011 57680 11236 8193 1.0113537 0 79 0
|
||||
83000 0.96941691 8173 0.22824759 37.029471 37.18745 2.9152799 13478 48 49 0 58712 57680 11236 8173 1.0168819 0 79 0
|
||||
84000 1.0770325 8186 0.22821292 37.006285 37.181802 5.0626072 13733 60 61 0 59433 57680 11236 8186 1.0177757 0 79 0
|
||||
85000 1.1959489 8175 0.2284266 37.021719 37.216615 5.3844747 13964 55 55 0 60226 57680 11236 8175 1.007371 0 79 0
|
||||
86000 1.035779 8204 0.22845952 37.053185 37.221979 7.5428558 13713 64 64 0 60982 57680 11236 8204 1.0110801 0 79 0
|
||||
87000 1.1878573 8204 0.22836412 37.012859 37.206436 3.1124447 13655 47 47 0 61668 57680 11236 8204 1.0034968 0 79 0
|
||||
88000 0.98402924 8206 0.22815704 37.012337 37.172698 10.613422 13947 56 56 0 62325 57680 11236 8206 1.0081468 0 79 0
|
||||
89000 0.83763529 8199 0.22807071 37.022127 37.158631 5.4628281 13966 50 50 0 63012 57680 11236 8199 0.99956322 0 79 0
|
||||
90000 1.1976672 8187 0.22849599 37.032745 37.227921 5.5583762 13903 43 43 0 63697 57680 11236 8187 1.0047573 0 79 0
|
||||
91000 0.94863742 8188 0.22818061 37.021945 37.176537 5.157692 13859 46 46 0 64382 57680 11236 8188 1.0041894 0 79 0
|
||||
92000 1.2038427 8172 0.22846103 37.026042 37.222224 6.685059 13675 57 57 0 65081 57680 11236 8172 1.0036906 0 79 0
|
||||
93000 0.95835618 8210 0.22828548 37.037446 37.193622 8.0038227 13826 57 58 0 65761 57680 11236 8210 1.0076646 0 79 0
|
||||
94000 1.2451267 8197 0.22856138 37.035665 37.238575 3.6305666 13918 62 62 0 66462 57680 11236 8197 1.0110913 0 79 0
|
||||
95000 0.82128549 8206 0.22809174 37.028218 37.162057 8.7024273 13817 44 44 0 67185 57680 11236 8206 1.0032224 0 79 0
|
||||
96000 0.83473128 8199 0.22820935 37.04519 37.18122 8.1258155 14167 54 54 0 67912 57680 11236 8199 1.0035561 0 79 0
|
||||
97000 0.98924493 8196 0.22847944 37.064014 37.225225 8.9964529 14039 48 51 0 68608 57680 11236 8196 1.0007515 0 79 0
|
||||
98000 1.1749668 8211 0.22879851 37.085733 37.27721 7.0283734 13850 58 59 0 69305 57680 11236 8211 0.99525651 0 79 0
|
||||
99000 1.3269705 8163 0.22890919 37.078994 37.295241 9.7962294 13885 63 63 0 69994 57680 11236 8163 1.011015 0 107 0
|
||||
100000 1.0020436 8171 0.22867221 37.093336 37.256632 4.9455304 14102 55 56 0 70707 57680 11236 8171 1.0072865 0 107 0
|
||||
Loop time of 33.9872 on 8 procs for 100000 steps with 43990 atoms
|
||||
|
||||
Pair time (%) = 0.379981 (1.11801)
|
||||
Neigh time (%) = 2.01801 (5.93757)
|
||||
Comm time (%) = 2.30255 (6.77476)
|
||||
Outpt time (%) = 0.00694308 (0.0204285)
|
||||
Other time (%) = 29.2797 (86.1492)
|
||||
|
||||
Nlocal: 5498.75 ave 6445 max 4431 min
|
||||
Histogram: 1 0 0 2 1 1 0 1 1 1
|
||||
Nghost: 62.5 ave 70 max 57 min
|
||||
Histogram: 3 0 0 1 1 0 1 0 1 1
|
||||
Neighs: 207 ave 365 max 92 min
|
||||
Histogram: 1 1 1 1 2 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1656
|
||||
Ave neighs/atom = 0.0376449
|
||||
Neighbor list builds = 5000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
@ -1,291 +0,0 @@
|
||||
LAMMPS (1 Feb 2014)
|
||||
# SRD viscosity demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
orthogonal box = (-13.2934 -13.2934 -0.5) to (13.2934 13.2934 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
270 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
270 settings made for mass
|
||||
group big type 1
|
||||
270 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 2.64859 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0.24721146
|
||||
100 0 3.291475 0 3.291475 0.69158089
|
||||
200 0 4.6176595 0 4.6176595 0.71737945
|
||||
300 0 7.0921814 0 7.0921814 1.2163497
|
||||
400 0 8.3666709 0 8.3666709 0.50645957
|
||||
500 0 10.630838 0 10.630838 0.72764487
|
||||
600 0 12.42157 0 12.42157 1.0130599
|
||||
700 0 14.349074 0 14.349074 0.74795509
|
||||
800 0 16.464746 0 16.464746 1.054549
|
||||
900 0 18.253108 0 18.253108 0.51551753
|
||||
1000 0 20.699563 0 20.699563 1.8084662
|
||||
Loop time of 0.0484946 on 8 procs for 1000 steps with 270 atoms
|
||||
|
||||
Pair time (%) = 0.00250834 (5.17242)
|
||||
Neigh time (%) = 0.000999629 (2.06132)
|
||||
Comm time (%) = 0.0154877 (31.9369)
|
||||
Outpt time (%) = 0.000273734 (0.564464)
|
||||
Other time (%) = 0.0292252 (60.2649)
|
||||
|
||||
Nlocal: 33.75 ave 42 max 22 min
|
||||
Histogram: 1 0 1 0 0 2 0 1 1 2
|
||||
Nghost: 23.375 ave 30 max 14 min
|
||||
Histogram: 1 0 1 0 0 2 1 0 1 2
|
||||
Neighs: 52.25 ave 69 max 27 min
|
||||
Histogram: 1 0 1 0 1 0 1 1 1 2
|
||||
|
||||
Total # of neighbors = 418
|
||||
Ave neighs/atom = 1.54815
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 60025 atoms
|
||||
|
||||
set type 2 mass 0.1
|
||||
60025 settings made for mass
|
||||
group small type 2
|
||||
60025 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
Deleted 16305 atoms, new total = 43990
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star.mp
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 43720 270
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 106 106 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250819 0.250819 1
|
||||
SRD per actual grid cell = 5.55866
|
||||
SRD viscosity = 0.235582
|
||||
big/SRD mass density ratio = 0.144099
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.19085 7.72582
|
||||
ave/max big velocity = 2.20262 5.4168
|
||||
Memory usage per processor = 7.83759 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.3197888 8196 0.2296966 37.208454 37.42353 7.4694369 14388 59 59 0 707 57680 11236 8196 1.0259754 0 5 0
|
||||
2000 1.5789784 8192 0.22993088 37.204387 37.461702 7.6252927 14352 56 56 0 1521 57680 11236 8192 1.0168955 0 7 0
|
||||
3000 1.286186 8153 0.2296947 37.213621 37.423222 8.8624394 14533 73 73 0 2299 57680 11236 8153 1.0109574 0 7 0
|
||||
4000 2.0862082 8194 0.23044604 37.20566 37.545635 7.8064365 14228 48 48 0 3068 57680 11236 8194 1.0046224 0 7 0
|
||||
5000 1.892401 8172 0.23019301 37.196017 37.504409 7.9041579 14290 55 55 0 3866 57680 11236 8172 1.005673 0 7 0
|
||||
6000 2.1063411 8138 0.23041636 37.197543 37.540799 4.8468885 13803 47 47 0 4638 57680 11236 8138 1.0083722 0 7 0
|
||||
7000 2.3549938 8174 0.23071159 37.205123 37.5889 6.5703154 13773 58 58 0 5398 57680 11236 8174 1.0039365 0 7 0
|
||||
8000 3.0660305 8216 0.23155654 37.226914 37.726563 11.977404 13898 65 65 0 6180 57680 11236 8216 0.99586836 0 7 0
|
||||
9000 3.1510761 8203 0.23143756 37.19367 37.707178 7.2978028 13815 54 54 0 6985 57680 11236 8203 0.99794556 0 7 0
|
||||
10000 2.7472522 8196 0.23096076 37.181796 37.629496 11.336568 14012 59 59 0 7812 57680 11236 8196 0.99210203 0 11 0
|
||||
11000 2.1776587 8186 0.23038876 37.181424 37.536302 9.2106614 14063 64 64 0 8627 57680 11236 8186 1.003993 0 11 0
|
||||
12000 3.0146734 8196 0.2312123 37.179198 37.670478 5.9303705 14077 60 60 0 9436 57680 11236 8196 0.98496016 0 23 0
|
||||
13000 3.0029829 8179 0.23150759 37.229214 37.718589 7.3329148 14116 74 74 0 10339 57680 11236 8179 1.0039911 0 23 0
|
||||
14000 3.2942972 8191 0.23166868 37.207985 37.744833 9.6428846 14019 56 57 0 11290 57680 11236 8191 0.99410574 0 23 0
|
||||
15000 3.8480961 8213 0.23228155 37.217589 37.844686 2.1025549 13746 68 68 0 12175 57680 11236 8213 1.0011325 0 23 0
|
||||
16000 3.2573043 8195 0.2316418 37.209634 37.740454 8.1255708 13682 55 55 0 13104 57680 11236 8195 1.0061399 0 23 0
|
||||
17000 3.3579037 8186 0.2315443 37.177356 37.72457 9.8606039 13833 54 54 0 14034 57680 11236 8186 1.004156 0 23 0
|
||||
18000 4.7903055 8194 0.23307181 37.192799 37.973441 3.8090185 13914 55 55 1 15012 57680 11236 8194 0.98633014 0 23 0
|
||||
19000 4.4696839 8183 0.23293212 37.222288 37.950681 7.1931333 13499 54 54 0 15960 57680 11236 8183 0.98359656 0 23 0
|
||||
20000 5.0239019 8126 0.23355887 37.234085 38.052794 5.1504203 13600 58 58 0 16972 57680 11236 8126 0.98555755 0 23 0
|
||||
21000 4.6595948 8155 0.23275722 37.162845 37.922186 9.0375076 13965 73 74 0 17966 57680 11236 8155 0.99574348 0 23 0
|
||||
22000 4.043444 8124 0.23247599 37.217434 37.876366 3.9265975 13584 53 53 2 18989 57680 11236 8124 0.9943952 0 23 0
|
||||
23000 4.9981028 8127 0.23314549 37.170939 37.985445 4.2352191 13589 47 47 0 19958 57680 11236 8127 0.99276741 0 47 0
|
||||
24000 4.7542655 8145 0.23295434 37.179533 37.954302 7.365415 13753 51 51 0 20955 57680 11236 8145 0.99024306 0 47 0
|
||||
25000 4.2987054 8177 0.23252979 37.184601 37.885131 10.735771 13536 58 58 0 21994 57680 11236 8177 0.99215977 0 47 0
|
||||
26000 4.4136261 8170 0.23331629 37.294015 38.013272 14.25925 13842 58 58 0 22979 57680 11236 8170 0.99283174 0 47 0
|
||||
27000 4.0546007 8173 0.23283443 37.274016 37.934766 6.22969 13877 51 51 0 23997 57680 11236 8173 0.98496361 0 47 0
|
||||
28000 4.5919614 8151 0.23364384 37.318319 38.066638 4.9917488 13836 60 61 1 25071 57680 11236 8151 0.99390956 0 47 0
|
||||
29000 4.8025535 8189 0.23313849 37.201667 37.984305 4.7895172 13978 46 47 0 26121 57680 11236 8189 0.99018295 0 47 0
|
||||
30000 4.2835226 8139 0.23247583 37.178284 37.87634 8.994878 13988 61 61 0 27141 57680 11236 8139 0.98735471 0 47 0
|
||||
31000 5.4049428 8133 0.23373767 37.201121 38.081927 7.6419291 13771 58 58 0 28207 57680 11236 8133 0.98354883 0 47 0
|
||||
32000 5.0299584 8177 0.23336211 37.201041 38.020738 8.1206741 14036 55 55 0 29303 57680 11236 8177 0.98239013 0 47 0
|
||||
33000 4.2993816 8158 0.23320229 37.29406 37.9947 10.745167 13583 51 51 0 30344 57680 11236 8158 0.98952524 0 47 0
|
||||
34000 5.8334257 8179 0.23458355 37.269109 38.219741 11.094625 13921 62 62 0 31432 57680 11236 8179 0.98822406 0 47 0
|
||||
35000 6.481318 8168 0.23501133 37.233224 38.289439 7.9397445 13942 56 56 0 32518 57680 11236 8168 0.98830425 0 47 0
|
||||
36000 4.967891 8186 0.23366927 37.261199 38.070782 8.3979019 13952 51 51 0 33626 57680 11236 8186 0.99579665 0 47 0
|
||||
37000 5.3458808 8145 0.2337339 37.210132 38.081312 5.4177865 13659 55 55 0 34715 57680 11236 8145 1.0009582 0 47 0
|
||||
38000 6.3597955 8159 0.23479285 37.217431 38.253842 6.1408411 13754 55 56 0 35754 57680 11236 8159 0.98853252 0 47 0
|
||||
39000 6.1217173 8195 0.23447066 37.203737 38.20135 9.6016075 13756 70 70 0 36807 57680 11236 8195 0.98652299 0 47 0
|
||||
40000 5.0218059 8159 0.23370899 37.258886 38.077254 6.6460004 13603 56 56 1 37933 57680 11236 8159 0.98674585 0 47 0
|
||||
41000 5.5873722 8138 0.23429215 37.26173 38.172265 1.4183057 13634 51 52 1 39050 57680 11236 8138 0.98833769 0 47 0
|
||||
42000 5.5502013 8170 0.23405343 37.228895 38.133372 7.8338637 13913 72 72 0 40105 57680 11236 8170 0.99124609 0 47 0
|
||||
43000 4.6854143 8161 0.23326283 37.241013 38.004562 7.857085 13759 48 48 0 41187 57680 11236 8161 0.99649848 0 47 0
|
||||
44000 6.3172352 8180 0.2348893 37.240081 38.269557 12.59288 13810 55 55 0 42292 57680 11236 8180 0.99164669 0 47 0
|
||||
45000 6.1213322 8166 0.23449878 37.208381 38.205931 6.3760889 13854 48 49 0 43406 57680 11236 8166 0.98981447 0 47 0
|
||||
46000 5.0015874 8195 0.23354809 37.235965 38.051038 10.992836 13962 62 62 0 44527 57680 11236 8195 0.99128184 0 47 0
|
||||
47000 5.0499615 8190 0.23376151 37.262854 38.085811 8.7985849 14105 64 64 0 45653 57680 11236 8190 0.99020272 0 47 0
|
||||
48000 5.202255 8170 0.23400688 37.278013 38.125788 4.7389097 13754 51 51 0 46705 57680 11236 8170 0.98792999 0 47 0
|
||||
49000 5.6144741 8167 0.23429848 37.258346 38.173297 6.3247626 13953 51 51 1 47846 57680 11236 8167 0.99270232 0 47 0
|
||||
50000 6.3027505 8145 0.2347122 37.213588 38.240703 6.4424496 13843 59 59 0 49061 57680 11236 8145 0.99810926 0 47 0
|
||||
51000 5.2050769 8154 0.23390178 37.26043 38.108665 6.6143765 13999 51 51 0 50075 57680 11236 8154 0.99525977 0 47 0
|
||||
52000 5.4749884 8175 0.23418567 37.262697 38.154917 8.7256782 13916 51 51 0 51249 57680 11236 8175 0.99508289 0 47 0
|
||||
53000 5.1367735 8158 0.23393299 37.276645 38.113748 9.3248422 13910 41 41 0 52381 57680 11236 8158 0.98956839 0 47 0
|
||||
54000 4.8680584 8211 0.23402832 37.335968 38.129281 4.8979582 14214 63 64 0 53439 57680 11236 8211 0.98838908 0 47 0
|
||||
55000 4.6223848 8167 0.23347097 37.285196 38.038473 6.1898955 14162 46 46 0 54504 57680 11236 8167 0.97935238 0 47 0
|
||||
56000 4.9075747 8168 0.23409393 37.340218 38.139971 12.20686 13980 60 60 0 55540 57680 11236 8168 0.99885966 0 47 0
|
||||
57000 4.8736147 8143 0.23354696 37.256636 38.050854 3.9348529 13857 59 59 0 56680 57680 11236 8143 0.98434054 0 47 0
|
||||
58000 5.6134201 8162 0.23393276 37.198932 38.113711 3.7493067 13866 55 55 2 57767 57680 11236 8162 0.99041155 0 47 0
|
||||
59000 5.440371 8197 0.23353392 37.162151 38.04873 4.1297786 13748 67 67 0 58894 57680 11236 8197 0.98824623 0 47 0
|
||||
60000 5.2754075 8148 0.23359083 37.198307 38.058003 7.1427242 13781 55 55 0 60028 57680 11236 8148 0.9831827 0 47 0
|
||||
61000 5.8228233 8153 0.23438274 37.23812 38.187025 8.8839625 14019 48 48 0 61204 57680 11236 8153 0.98566731 0 47 0
|
||||
62000 5.7623285 8129 0.23480056 37.316052 38.255098 9.992341 13791 67 68 0 62385 57680 11236 8129 0.97338459 0 47 0
|
||||
63000 6.095315 8178 0.23455792 37.222257 38.215567 10.722535 14210 54 54 0 63448 57680 11236 8178 0.98135973 0 47 0
|
||||
64000 5.2494942 8189 0.23380158 37.236866 38.092339 4.4010329 13869 51 51 0 64538 57680 11236 8189 0.98071569 0 47 0
|
||||
65000 5.6534858 8151 0.23405328 37.212039 38.133348 8.9144953 14065 53 53 0 65661 57680 11236 8151 0.99589337 0 47 0
|
||||
66000 5.3999138 8165 0.23453061 37.33113 38.211116 7.3102657 13994 61 62 0 66785 57680 11236 8165 0.98715854 0 47 0
|
||||
67000 6.3619419 8183 0.23459518 37.184875 38.221636 4.0425684 13859 49 49 0 67944 57680 11236 8183 0.98479883 0 47 0
|
||||
68000 6.2170116 8157 0.23470153 37.225822 38.238965 9.3090925 13598 50 50 0 69121 57680 11236 8157 0.98683618 0 47 0
|
||||
69000 6.8545121 8179 0.23542272 37.239433 38.356465 9.4175179 13911 59 59 0 70316 57680 11236 8179 0.99828763 0 47 0
|
||||
70000 5.1476232 8154 0.23389653 37.268937 38.107809 7.6438157 13882 55 55 0 71380 57680 11236 8154 0.99088995 0 47 0
|
||||
71000 5.9284504 8161 0.23499148 37.320087 38.286205 9.1242845 13968 60 60 0 72478 57680 11236 8161 0.98627289 0 47 0
|
||||
72000 5.8044136 8180 0.23473312 37.298207 38.244111 6.6084298 14066 56 56 0 73653 57680 11236 8180 0.97959812 0 47 0
|
||||
73000 5.3690655 8148 0.23424676 37.289911 38.16487 8.7025002 14433 55 55 1 74740 57680 11236 8148 0.97949605 0 47 0
|
||||
74000 4.8144157 8192 0.23361625 37.277572 38.062144 7.6685178 14425 58 58 1 75918 57680 11236 8192 0.98949387 0 47 0
|
||||
75000 4.9424688 8143 0.23362551 37.258213 38.063652 5.5882668 13938 42 42 0 77080 57680 11236 8143 0.99602516 0 47 0
|
||||
76000 6.3017203 8178 0.23500247 37.261048 38.287995 5.2760401 13952 47 47 0 78240 57680 11236 8178 0.98484281 0 47 0
|
||||
77000 5.3086333 8208 0.23389726 37.242817 38.107928 4.034731 14052 47 47 0 79331 57680 11236 8208 0.9896033 0 47 0
|
||||
78000 6.1152265 8157 0.23546115 37.366171 38.362726 11.521489 13980 58 58 0 80446 57680 11236 8157 0.98562154 0 47 0
|
||||
79000 6.5034669 8173 0.23569944 37.341726 38.40155 5.0939756 14030 74 74 0 81663 57680 11236 8173 0.98837711 0 47 0
|
||||
80000 6.1688245 8182 0.23495003 37.274162 38.279451 6.3337593 14292 50 50 0 82872 57680 11236 8182 0.99316806 0 47 0
|
||||
81000 6.3818913 8189 0.23516767 37.274899 38.314911 9.0232294 14259 56 56 0 84072 57680 11236 8189 0.98467136 0 47 0
|
||||
82000 6.502454 8171 0.23498158 37.224932 38.284591 7.6685939 13970 63 63 0 85190 57680 11236 8171 0.99511647 0 47 0
|
||||
83000 7.2245962 8142 0.23564338 37.215075 38.392416 6.0363083 13789 61 61 0 86416 57680 11236 8142 0.99223565 0 47 0
|
||||
84000 6.3529888 8192 0.23477435 37.215526 38.250828 7.2109855 14062 52 52 0 87555 57680 11236 8192 0.98623425 0 47 0
|
||||
85000 6.5185235 8177 0.23516364 37.251976 38.314254 5.266764 14325 52 53 0 88732 57680 11236 8177 0.97895516 0 47 0
|
||||
86000 5.742959 8170 0.23432816 37.242243 38.178133 6.0834874 13922 48 48 0 89836 57680 11236 8170 0.99203022 0 47 0
|
||||
87000 6.548676 8177 0.23495538 37.213132 38.280324 6.2502744 14147 48 48 0 91035 57680 11236 8177 0.98829721 0 47 0
|
||||
88000 5.9500587 8193 0.23446634 37.231006 38.200645 6.2196893 13960 44 44 0 92206 57680 11236 8193 0.98956808 0 47 0
|
||||
89000 5.0591447 8174 0.23386574 37.278339 38.102793 11.164066 14071 54 54 0 93437 57680 11236 8174 0.99827748 0 47 0
|
||||
90000 6.4930795 8181 0.23544182 37.301445 38.359576 6.6167028 14183 63 63 1 94640 57680 11236 8181 0.99559871 0 47 0
|
||||
91000 6.489104 8187 0.23523152 37.267829 38.325313 6.4932786 14223 51 51 1 95718 57680 11236 8187 0.99090796 0 47 0
|
||||
92000 6.3543839 8184 0.23502776 37.256587 38.292116 7.1553807 14265 66 66 1 96903 57680 11236 8184 0.98979354 0 47 0
|
||||
93000 5.3818591 8195 0.23393122 37.236417 38.11346 7.9445503 14327 70 70 0 98138 57680 11236 8195 1.0030252 0 47 0
|
||||
94000 5.6818206 8171 0.2343696 37.258958 38.184885 5.7311019 13943 63 63 0 99306 57680 11236 8171 0.99691591 0 47 0
|
||||
95000 4.8295204 8160 0.23371941 37.291918 38.078951 4.5703653 13682 48 48 1 100491 57680 11236 8160 1.0078235 0 47 0
|
||||
96000 6.7415726 8191 0.23539566 37.253429 38.352056 11.837168 13783 53 53 1 101761 57680 11236 8191 1.0010125 0 49 0
|
||||
97000 6.5298825 8160 0.2354153 37.291126 38.355255 7.6012271 13688 65 65 0 103010 57680 11236 8160 0.99694671 0 49 0
|
||||
98000 6.2804965 8175 0.23496877 37.259015 38.282504 5.4636503 14041 55 55 0 104259 57680 11236 8175 1.0042653 0 49 0
|
||||
99000 5.7684681 8173 0.2344998 37.26605 38.206096 1.7807753 14082 58 59 0 105418 57680 11236 8173 0.99124491 0 49 0
|
||||
100000 6.1371898 8170 0.23495644 37.28036 38.280495 7.7665232 13908 53 53 0 106633 57680 11236 8170 0.98281247 0 49 0
|
||||
Loop time of 34.1892 on 8 procs for 100000 steps with 43990 atoms
|
||||
|
||||
Pair time (%) = 0.361362 (1.05695)
|
||||
Neigh time (%) = 2.01143 (5.88324)
|
||||
Comm time (%) = 2.27139 (6.64359)
|
||||
Outpt time (%) = 0.00694269 (0.0203067)
|
||||
Other time (%) = 29.5381 (86.3959)
|
||||
|
||||
Nlocal: 5498.75 ave 6478 max 4726 min
|
||||
Histogram: 2 0 1 0 1 2 1 0 0 1
|
||||
Nghost: 52.875 ave 59 max 44 min
|
||||
Histogram: 1 0 1 0 1 0 1 0 2 2
|
||||
Neighs: 186.25 ave 293 max 81 min
|
||||
Histogram: 1 0 1 3 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 1490
|
||||
Ave neighs/atom = 0.0338713
|
||||
Neighbor list builds = 5000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
321
examples/ASPHERE/star/log.1Feb24.star.g++.1
Normal file
321
examples/ASPHERE/star/log.1Feb24.star.g++.1
Normal file
@ -0,0 +1,321 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD diffusion demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
Reading data file ...
|
||||
orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
270 atoms
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
270 settings made for mass
|
||||
group big type 1
|
||||
270 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
compute tbig all temp/sphere
|
||||
thermo_modify temp tbig
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42
|
||||
ghost atom cutoff = 1.42
|
||||
binsize = 0.71, bins = 38 38 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.562 | 5.562 | 5.562 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.3101488 0 0 0.21350573 0.32876464
|
||||
100 5.0954142 3.291475 0 4.1218387 1.0087565
|
||||
200 13.041252 4.6176595 0 6.7429006 1.5291618
|
||||
300 11.912727 7.0921814 0 9.0335147 1.9578844
|
||||
400 17.60886 8.3666709 0 11.236263 1.602563
|
||||
500 16.786375 10.630838 0 13.366396 1.7725508
|
||||
600 18.470347 12.42157 0 15.431552 2.1627885
|
||||
700 19.39794 14.349074 0 17.510219 1.9554238
|
||||
800 19.082984 16.464746 0 19.574566 2.2424126
|
||||
900 20.702091 18.253108 0 21.626782 1.8041661
|
||||
1000 18.299191 20.699563 0 23.681654 2.9475408
|
||||
Loop time of 0.0585091 on 1 procs for 1000 steps with 270 atoms
|
||||
|
||||
Performance: 7383466.593 tau/day, 17091.358 timesteps/s, 4.615 Matom-step/s
|
||||
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.017165 | 0.017165 | 0.017165 | 0.0 | 29.34
|
||||
Neigh | 0.0058479 | 0.0058479 | 0.0058479 | 0.0 | 9.99
|
||||
Comm | 0.0028221 | 0.0028221 | 0.0028221 | 0.0 | 4.82
|
||||
Output | 0.00017384 | 0.00017384 | 0.00017384 | 0.0 | 0.30
|
||||
Modify | 0.03015 | 0.03015 | 0.03015 | 0.0 | 51.53
|
||||
Other | | 0.00235 | | | 4.02
|
||||
|
||||
Nlocal: 270 ave 270 max 270 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 73 ave 73 max 73 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 418 ave 418 max 418 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 418
|
||||
Ave neighs/atom = 1.5481481
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
|
||||
create_atoms 2 region plane
|
||||
Created 60025 atoms
|
||||
using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
|
||||
create_atoms CPU = 0.013 seconds
|
||||
|
||||
set type 2 mass 0.1
|
||||
Setting atom values ...
|
||||
60025 settings made for mass
|
||||
group small type 2
|
||||
60025 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 19 19 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 16305 atoms, new total = 43990
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
uncompute tbig
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 43720 270
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 106 106 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
|
||||
SRD per actual grid cell = 5.5586635
|
||||
SRD viscosity = 0.23558168
|
||||
big/SRD mass density ratio = 0.14409881
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.1908497 7.725824
|
||||
ave/max big velocity = 2.202625 5.4167964
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 26.586808, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 41.29 | 41.29 | 41.29 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.2074332 8227 0.22959643 37.210444 37.407211 7.9007359 14317 47 47 0 649 28900 11236 8227 1.0260288 0 3 0
|
||||
2000 1.2044605 8206 0.22945824 37.188414 37.384697 5.8738384 14470 63 63 0 1423 28900 11236 8206 1.018589 0 4 0
|
||||
3000 1.1060368 8226 0.22936549 37.189341 37.369584 4.7013136 14255 51 51 0 2207 28900 11236 8226 1.0007203 0 4 0
|
||||
4000 1.2395587 8236 0.2294891 37.187723 37.389725 5.7916781 14371 56 56 0 2916 28900 11236 8236 1.0229966 0 4 0
|
||||
5000 1.3332555 8236 0.22962818 37.195112 37.412383 10.662157 14373 61 61 0 3740 28900 11236 8236 1.0094713 0 4 0
|
||||
6000 1.2991744 8192 0.22957221 37.191547 37.403264 1.2016626 14145 56 58 0 4425 28900 11236 8192 1.0215234 0 4 0
|
||||
7000 1.0110737 8147 0.22923336 37.18329 37.348057 6.2493424 14200 59 59 0 5102 28900 11236 8147 1.0163405 0 4 0
|
||||
8000 0.79508387 8168 0.22908516 37.194343 37.323912 9.832591 14355 45 45 0 5839 28900 11236 8168 1.0063207 0 4 0
|
||||
9000 1.0340542 8207 0.2292515 37.1825 37.351013 11.458942 14220 54 54 0 6606 28900 11236 8207 1.0074421 0 4 0
|
||||
10000 0.96342976 8202 0.22912995 37.174206 37.33121 1.7523017 14308 53 53 0 7379 28900 11236 8202 1.0126923 0 4 0
|
||||
Loop time of 18.5504 on 1 procs for 10000 steps with 43990 atoms
|
||||
|
||||
Performance: 46575.737 tau/day, 539.071 timesteps/s, 23.714 Matom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.21961 | 0.21961 | 0.21961 | 0.0 | 1.18
|
||||
Neigh | 0.055763 | 0.055763 | 0.055763 | 0.0 | 0.30
|
||||
Comm | 0.22073 | 0.22073 | 0.22073 | 0.0 | 1.19
|
||||
Output | 0.0013822 | 0.0013822 | 0.0013822 | 0.0 | 0.01
|
||||
Modify | 17.872 | 17.872 | 17.872 | 0.0 | 96.34
|
||||
Other | | 0.1812 | | | 0.98
|
||||
|
||||
Nlocal: 43990 ave 43990 max 43990 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 138 ave 138 max 138 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1587 ave 1587 max 1587 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1587
|
||||
Ave neighs/atom = 0.036076381
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:20
|
||||
321
examples/ASPHERE/star/log.1Feb24.star.g++.4
Normal file
321
examples/ASPHERE/star/log.1Feb24.star.g++.4
Normal file
@ -0,0 +1,321 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD diffusion demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
Reading data file ...
|
||||
orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
270 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
270 settings made for mass
|
||||
group big type 1
|
||||
270 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
compute tbig all temp/sphere
|
||||
thermo_modify temp tbig
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42
|
||||
ghost atom cutoff = 1.42
|
||||
binsize = 0.71, bins = 38 38 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.554 | 5.554 | 5.555 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.3101488 0 0 0.21350573 0.32876464
|
||||
100 5.0954142 3.291475 0 4.1218387 1.0087565
|
||||
200 13.041252 4.6176595 0 6.7429006 1.5291618
|
||||
300 11.912727 7.0921814 0 9.0335147 1.9578844
|
||||
400 17.60886 8.3666709 0 11.236263 1.602563
|
||||
500 16.786375 10.630838 0 13.366396 1.7725508
|
||||
600 18.470347 12.42157 0 15.431552 2.1627885
|
||||
700 19.39794 14.349074 0 17.510219 1.9554238
|
||||
800 19.082984 16.464746 0 19.574566 2.2424126
|
||||
900 20.702091 18.253108 0 21.626782 1.8041661
|
||||
1000 18.299191 20.699563 0 23.681654 2.9475408
|
||||
Loop time of 0.0312248 on 4 procs for 1000 steps with 270 atoms
|
||||
|
||||
Performance: 13835169.963 tau/day, 32025.856 timesteps/s, 8.647 Matom-step/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0026978 | 0.0031211 | 0.0033489 | 0.5 | 10.00
|
||||
Neigh | 0.0011292 | 0.0013054 | 0.0014446 | 0.3 | 4.18
|
||||
Comm | 0.010095 | 0.010474 | 0.010975 | 0.3 | 33.54
|
||||
Output | 0.00019592 | 0.00021948 | 0.00027642 | 0.0 | 0.70
|
||||
Modify | 0.013333 | 0.013668 | 0.013952 | 0.2 | 43.77
|
||||
Other | | 0.002437 | | | 7.80
|
||||
|
||||
Nlocal: 67.5 ave 80 max 54 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 29.75 ave 33 max 26 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Neighs: 104.5 ave 135 max 72 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 418
|
||||
Ave neighs/atom = 1.5481481
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
|
||||
create_atoms 2 region plane
|
||||
Created 60025 atoms
|
||||
using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
|
||||
create_atoms CPU = 0.003 seconds
|
||||
|
||||
set type 2 mass 0.1
|
||||
Setting atom values ...
|
||||
60025 settings made for mass
|
||||
group small type 2
|
||||
60025 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 19 19 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 16305 atoms, new total = 43990
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
uncompute tbig
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 43720 270
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 106 106 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
|
||||
SRD per actual grid cell = 5.5586635
|
||||
SRD viscosity = 0.23558168
|
||||
big/SRD mass density ratio = 0.14409881
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.1908497 7.725824
|
||||
ave/max big velocity = 2.202625 5.4167964
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 26.586808, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 14.19 | 14.19 | 14.2 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.4057114 8217 0.22974151 37.20177 37.430849 11.548865 14197 56 57 0 682 42436 11236 8217 1.0187465 0 3 0
|
||||
2000 1.0468288 8223 0.22932205 37.191914 37.362508 4.8322766 14185 60 60 0 1452 42436 11236 8223 1.0271433 0 64 0
|
||||
3000 0.89541606 8240 0.22921893 37.199787 37.345707 9.7555289 14770 60 60 0 2175 42436 11236 8240 1.0157844 0 64 0
|
||||
4000 1.021344 8222 0.22920858 37.177579 37.344021 6.2834235 14480 50 50 0 2951 42436 11236 8222 1.0130315 0 64 0
|
||||
5000 1.045809 8222 0.2294309 37.209813 37.380241 2.8847497 14109 59 60 0 3667 42436 11236 8222 1.0126872 0 64 0
|
||||
6000 1.1527336 8227 0.22933212 37.176296 37.364149 5.4760843 14597 42 42 0 4418 42436 11236 8227 1.0188272 0 64 0
|
||||
7000 1.1799559 8216 0.22941075 37.18467 37.376959 10.243848 14281 57 57 0 5154 42436 11236 8216 1.0063617 0 64 0
|
||||
8000 1.1913762 8188 0.22940126 37.181263 37.375413 5.7338518 14497 47 47 0 5878 42436 11236 8188 1.0076169 0 64 0
|
||||
9000 1.0587094 8230 0.22928172 37.183406 37.355936 5.7323116 14267 62 62 0 6550 42436 11236 8230 1.0108237 0 64 0
|
||||
10000 1.0359117 8165 0.22944086 37.21305 37.381865 9.4246373 14016 52 52 0 7246 42436 11236 8165 1.0147132 0 64 0
|
||||
Loop time of 6.61179 on 4 procs for 10000 steps with 43990 atoms
|
||||
|
||||
Performance: 130675.562 tau/day, 1512.449 timesteps/s, 66.533 Matom-step/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 | 0.041077 | 0.059027 | 0.07409 | 4.8 | 0.89
|
||||
Neigh | 0.015706 | 0.017829 | 0.019903 | 1.1 | 0.27
|
||||
Comm | 0.23742 | 0.25326 | 0.26722 | 2.1 | 3.83
|
||||
Output | 0.00073333 | 0.00077549 | 0.00084859 | 0.0 | 0.01
|
||||
Modify | 6.1477 | 6.174 | 6.2149 | 1.0 | 93.38
|
||||
Other | | 0.1069 | | | 1.62
|
||||
|
||||
Nlocal: 10997.5 ave 11924 max 10204 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Nghost: 64.25 ave 71 max 56 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Neighs: 395.5 ave 497 max 271 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1582
|
||||
Ave neighs/atom = 0.035962719
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
322
examples/ASPHERE/star/log.1Feb24.star.mp.g++.1
Normal file
322
examples/ASPHERE/star/log.1Feb24.star.mp.g++.1
Normal file
@ -0,0 +1,322 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD viscosity demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
Reading data file ...
|
||||
orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
270 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
270 settings made for mass
|
||||
group big type 1
|
||||
270 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
compute tbig all temp/sphere
|
||||
thermo_modify temp tbig
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42
|
||||
ghost atom cutoff = 1.42
|
||||
binsize = 0.71, bins = 38 38 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.562 | 5.562 | 5.562 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.3101488 0 0 0.21350573 0.32876464
|
||||
100 5.0954142 3.291475 0 4.1218387 1.0087565
|
||||
200 13.041252 4.6176595 0 6.7429006 1.5291618
|
||||
300 11.912727 7.0921814 0 9.0335147 1.9578844
|
||||
400 17.60886 8.3666709 0 11.236263 1.602563
|
||||
500 16.786375 10.630838 0 13.366396 1.7725508
|
||||
600 18.470347 12.42157 0 15.431552 2.1627885
|
||||
700 19.39794 14.349074 0 17.510219 1.9554238
|
||||
800 19.082984 16.464746 0 19.574566 2.2424126
|
||||
900 20.702091 18.253108 0 21.626782 1.8041661
|
||||
1000 18.299191 20.699563 0 23.681654 2.9475408
|
||||
Loop time of 0.0474374 on 1 procs for 1000 steps with 270 atoms
|
||||
|
||||
Performance: 9106745.092 tau/day, 21080.428 timesteps/s, 5.692 Matom-step/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.01287 | 0.01287 | 0.01287 | 0.0 | 27.13
|
||||
Neigh | 0.0050573 | 0.0050573 | 0.0050573 | 0.0 | 10.66
|
||||
Comm | 0.0024616 | 0.0024616 | 0.0024616 | 0.0 | 5.19
|
||||
Output | 0.00025461 | 0.00025461 | 0.00025461 | 0.0 | 0.54
|
||||
Modify | 0.024714 | 0.024714 | 0.024714 | 0.0 | 52.10
|
||||
Other | | 0.00208 | | | 4.38
|
||||
|
||||
Nlocal: 270 ave 270 max 270 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 73 ave 73 max 73 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 418 ave 418 max 418 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 418
|
||||
Ave neighs/atom = 1.5481481
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
|
||||
create_atoms 2 region plane
|
||||
Created 60025 atoms
|
||||
using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
|
||||
create_atoms CPU = 0.014 seconds
|
||||
|
||||
set type 2 mass 0.1
|
||||
Setting atom values ...
|
||||
60025 settings made for mass
|
||||
group small type 2
|
||||
60025 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 19 19 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 16305 atoms, new total = 43990
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
uncompute tbig
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star.mp
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 43720 270
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 106 106 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
|
||||
SRD per actual grid cell = 5.5586635
|
||||
SRD viscosity = 0.23558168
|
||||
big/SRD mass density ratio = 0.14409881
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.1908497 7.725824
|
||||
ave/max big velocity = 2.202625 5.4167964
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 26.586808, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 41.29 | 41.29 | 41.29 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 0.82328749 8250 0.22908506 37.18973 37.323895 6.0611499 14546 54 54 0 691 28900 11236 8250 1.025654 0 3 0
|
||||
2000 1.314397 8198 0.22953802 37.183497 37.397695 7.6050033 14165 65 65 0 1503 28900 11236 8198 1.0137885 0 3 0
|
||||
3000 1.4327928 8174 0.22973765 37.196727 37.430219 4.8441566 14378 43 43 0 2274 28900 11236 8174 1.0052401 0 5 0
|
||||
4000 1.9637993 8194 0.23036966 37.213164 37.533191 4.9697216 14203 51 51 1 3241 28900 11236 8194 1.0129187 0 245 0
|
||||
5000 1.6886675 8206 0.22987561 37.177507 37.452697 10.972628 14155 56 56 0 4073 28900 11236 8206 1.0024406 0 245 0
|
||||
6000 1.7377657 8197 0.23000322 37.190296 37.473487 6.3971042 14331 57 57 0 4929 28900 11236 8197 1.0094945 0 245 0
|
||||
7000 2.4106224 8199 0.23083719 37.216521 37.609363 5.1070917 14144 49 49 0 5822 28900 11236 8199 1.0074275 0 245 0
|
||||
8000 2.5161884 8202 0.2306663 37.171475 37.581521 12.156127 14263 67 67 0 6667 28900 11236 8202 1.006502 0 245 0
|
||||
9000 2.9100148 8188 0.23124828 37.202115 37.67634 6.1326598 14171 66 67 0 7443 28900 11236 8188 0.99544201 0 245 0
|
||||
10000 3.4714177 8206 0.23192306 37.220567 37.78628 5.1293943 14100 48 49 0 8272 28900 11236 8206 1.0022763 0 245 0
|
||||
Loop time of 17.933 on 1 procs for 10000 steps with 43990 atoms
|
||||
|
||||
Performance: 48179.444 tau/day, 557.632 timesteps/s, 24.530 Matom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.22008 | 0.22008 | 0.22008 | 0.0 | 1.23
|
||||
Neigh | 0.054046 | 0.054046 | 0.054046 | 0.0 | 0.30
|
||||
Comm | 0.20917 | 0.20917 | 0.20917 | 0.0 | 1.17
|
||||
Output | 0.001317 | 0.001317 | 0.001317 | 0.0 | 0.01
|
||||
Modify | 17.275 | 17.275 | 17.275 | 0.0 | 96.33
|
||||
Other | | 0.1731 | | | 0.97
|
||||
|
||||
Nlocal: 43990 ave 43990 max 43990 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 122 ave 122 max 122 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1569 ave 1569 max 1569 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1569
|
||||
Ave neighs/atom = 0.035667197
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:19
|
||||
322
examples/ASPHERE/star/log.1Feb24.star.mp.g++.4
Normal file
322
examples/ASPHERE/star/log.1Feb24.star.mp.g++.4
Normal file
@ -0,0 +1,322 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# SRD viscosity demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol ghost yes
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
Reading data file ...
|
||||
orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
270 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
270 settings made for mass
|
||||
group big type 1
|
||||
270 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
compute tbig all temp/sphere
|
||||
thermo_modify temp tbig
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42
|
||||
ghost atom cutoff = 1.42
|
||||
binsize = 0.71, bins = 38 38 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.554 | 5.554 | 5.555 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.3101488 0 0 0.21350573 0.32876464
|
||||
100 5.0954142 3.291475 0 4.1218387 1.0087565
|
||||
200 13.041252 4.6176595 0 6.7429006 1.5291618
|
||||
300 11.912727 7.0921814 0 9.0335147 1.9578844
|
||||
400 17.60886 8.3666709 0 11.236263 1.602563
|
||||
500 16.786375 10.630838 0 13.366396 1.7725508
|
||||
600 18.470347 12.42157 0 15.431552 2.1627885
|
||||
700 19.39794 14.349074 0 17.510219 1.9554238
|
||||
800 19.082984 16.464746 0 19.574566 2.2424126
|
||||
900 20.702091 18.253108 0 21.626782 1.8041661
|
||||
1000 18.299191 20.699563 0 23.681654 2.9475408
|
||||
Loop time of 0.0311841 on 4 procs for 1000 steps with 270 atoms
|
||||
|
||||
Performance: 13853197.664 tau/day, 32067.587 timesteps/s, 8.658 Matom-step/s
|
||||
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0027957 | 0.0031644 | 0.0035219 | 0.5 | 10.15
|
||||
Neigh | 0.001171 | 0.0012862 | 0.0014036 | 0.3 | 4.12
|
||||
Comm | 0.0099068 | 0.010544 | 0.011053 | 0.4 | 33.81
|
||||
Output | 0.00014281 | 0.00016091 | 0.00020823 | 0.0 | 0.52
|
||||
Modify | 0.013319 | 0.013618 | 0.014047 | 0.2 | 43.67
|
||||
Other | | 0.002411 | | | 7.73
|
||||
|
||||
Nlocal: 67.5 ave 80 max 54 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 29.75 ave 33 max 26 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Neighs: 104.5 ave 135 max 72 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 418
|
||||
Ave neighs/atom = 1.5481481
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
|
||||
create_atoms 2 region plane
|
||||
Created 60025 atoms
|
||||
using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
|
||||
create_atoms CPU = 0.003 seconds
|
||||
|
||||
set type 2 mass 0.1
|
||||
Setting atom values ...
|
||||
60025 settings made for mass
|
||||
group small type 2
|
||||
60025 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 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 = 19 19 1
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 16305 atoms, new total = 43990
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
uncompute tbig
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star.mp
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 43720 270
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.063245553
|
||||
SRD max distance & max velocity = 0.25298221 12.649111
|
||||
SRD grid counts: 106 106 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
|
||||
SRD per actual grid cell = 5.5586635
|
||||
SRD viscosity = 0.23558168
|
||||
big/SRD mass density ratio = 0.14409881
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.1908497 7.725824
|
||||
ave/max big velocity = 2.202625 5.4167964
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 26.586808, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 14.19 | 14.19 | 14.2 Mbytes
|
||||
Step Temp f_2[8] TotEng v_pebig v_ebig Press 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[12]
|
||||
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.3506473 8186 0.22968182 37.201018 37.421123 5.6398923 14572 54 54 0 654 42436 11236 8186 1.0228728 0 3 0
|
||||
2000 0.99412905 8212 0.22952823 37.234094 37.3961 8.5863689 14257 69 69 0 1394 42436 11236 8212 1.0206297 0 12 0
|
||||
3000 1.4469134 8192 0.22970951 37.189841 37.425634 8.0408437 14439 53 53 0 2178 42436 11236 8192 1.0121272 0 12 0
|
||||
4000 1.6112802 8172 0.2303679 37.270324 37.532903 8.3379947 14098 57 57 0 2992 42436 11236 8172 1.0171443 0 12 0
|
||||
5000 2.0436283 8191 0.23016186 37.166298 37.499334 7.1370191 14030 49 49 0 3804 42436 11236 8191 1.0054513 0 12 0
|
||||
6000 2.2894073 8184 0.2303867 37.162878 37.535967 7.6496143 13970 50 50 0 4662 42436 11236 8184 1.0084738 0 12 0
|
||||
7000 2.1640822 8183 0.23045121 37.193812 37.546477 7.1526683 13926 56 57 0 5445 42436 11236 8183 1.0046108 0 15 0
|
||||
8000 2.8851243 8199 0.23121762 37.201176 37.671344 9.1644504 13849 58 58 0 6237 42436 11236 8199 1.0081629 0 15 0
|
||||
9000 2.6422092 8180 0.23070839 37.157795 37.588377 2.4816571 13651 70 70 0 7007 42436 11236 8180 1.0089869 0 15 0
|
||||
10000 2.7121051 8189 0.23087145 37.172972 37.614945 11.176036 13901 63 64 0 7845 42436 11236 8189 1.0023484 0 15 0
|
||||
Loop time of 6.56969 on 4 procs for 10000 steps with 43990 atoms
|
||||
|
||||
Performance: 131513.146 tau/day, 1522.143 timesteps/s, 66.959 Matom-step/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.037869 | 0.059232 | 0.073664 | 5.4 | 0.90
|
||||
Neigh | 0.015688 | 0.017835 | 0.019891 | 1.1 | 0.27
|
||||
Comm | 0.22905 | 0.24375 | 0.26098 | 2.3 | 3.71
|
||||
Output | 0.00069058 | 0.00071614 | 0.00078869 | 0.0 | 0.01
|
||||
Modify | 6.1124 | 6.1385 | 6.1881 | 1.2 | 93.44
|
||||
Other | | 0.1096 | | | 1.67
|
||||
|
||||
Nlocal: 10997.5 ave 12305 max 10259 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 58.25 ave 73 max 48 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 402.75 ave 520 max 207 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
|
||||
Total # of neighbors = 1611
|
||||
Ave neighs/atom = 0.03662196
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
@ -1,107 +1,107 @@
|
||||
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
|
||||
|
||||
units lj
|
||||
atom_style tri
|
||||
atom_modify first big map yes
|
||||
units lj
|
||||
atom_style tri
|
||||
atom_modify first big map yes
|
||||
|
||||
read_data data.tri.srd
|
||||
read_data data.tri.srd
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sc 0.4
|
||||
region box block INF INF INF INF INF INF
|
||||
lattice sc 20.0
|
||||
create_atoms 2 region box
|
||||
lattice sc 0.4
|
||||
region box block INF INF INF INF INF INF
|
||||
lattice sc 20.0
|
||||
create_atoms 2 region box
|
||||
|
||||
group big type 1
|
||||
group small type 2
|
||||
set group small mass 0.01
|
||||
group big type 1
|
||||
group small type 2
|
||||
set group small mass 0.01
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
delete_atoms overlap 1.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule/intra big include big
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule/intra big include big
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style tri/lj 3.5
|
||||
pair_coeff 1 1 0.1 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
pair_style tri/lj 3.5
|
||||
pair_coeff 1 1 0.1 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip inside ignore
|
||||
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip inside ignore
|
||||
|
||||
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
|
||||
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute_modify tbig extra/dof -4500
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
|
||||
thermo_modify temp tbig
|
||||
thermo 100
|
||||
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
|
||||
thermo_modify temp tbig
|
||||
|
||||
compute 10 all property/atom corner1x corner1y corner1z &
|
||||
corner2x corner2y corner2z corner3x corner3y corner3z
|
||||
compute 10 all property/atom corner1x corner1y corner1z &
|
||||
corner2x corner2y corner2z corner3x corner3y corner3z
|
||||
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.tri.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] &
|
||||
# c_10[7] c_10[8] c_10[9]
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.tri.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] &
|
||||
# c_10[7] c_10[8] c_10[9]
|
||||
|
||||
run 10000
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip tstat yes inside ignore
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip tstat yes inside ignore
|
||||
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.tri.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] &
|
||||
# c_10[7] c_10[8] c_10[9]
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.tri.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] &
|
||||
# c_10[7] c_10[8] c_10[9]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 40000
|
||||
run 2000
|
||||
|
||||
@ -1,812 +0,0 @@
|
||||
LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-114-gdad8081d55-modified)
|
||||
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:537)
|
||||
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
|
||||
|
||||
units lj
|
||||
atom_style tri
|
||||
atom_modify first big map yes
|
||||
|
||||
read_data data.tri.srd
|
||||
Reading data file ...
|
||||
orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1500 atoms
|
||||
1500 triangles
|
||||
read_data CPU = 0.007 seconds
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block INF INF INF INF INF INF
|
||||
lattice sc 20.0
|
||||
Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
|
||||
create_atoms 2 region box
|
||||
Created 91125 atoms
|
||||
using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
group big type 1
|
||||
1500 atoms in group big
|
||||
group small type 2
|
||||
91125 atoms in group small
|
||||
set group small mass 0.01
|
||||
Setting atom values ...
|
||||
91125 settings made for mass
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.8
|
||||
ghost atom cutoff = 1.8
|
||||
binsize = 0.9, bins = 19 19 19
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:312)
|
||||
Deleted 76354 atoms, new total = 16271
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule/intra big include big
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style tri/lj 3.5
|
||||
pair_coeff 1 1 0.1 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
|
||||
create bodies CPU = 0.000 seconds
|
||||
125 rigid bodies with 1500 atoms
|
||||
1.8601881 = max distance from body owner to body atom
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
|
||||
|
||||
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute_modify tbig extra/dof -4500
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:527)
|
||||
|
||||
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
|
||||
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:71)
|
||||
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:405)
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 2.9202881 0.87320391
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 17 17 17
|
||||
SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
|
||||
SRD per actual grid cell = -3.9971745
|
||||
SRD viscosity = -34.162587
|
||||
big/SRD mass density ratio = -3.3753691
|
||||
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 19.970837 35.150443
|
||||
ave/max big velocity = 0 0
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.8
|
||||
ghost atom cutoff = 3.8
|
||||
binsize = 16.874681, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tri/lj, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/newton
|
||||
stencil: half/multi/3d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 125.9 | 126.4 | 126.7 Mbytes
|
||||
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
|
||||
0 0 1.4401779 0 -0.15917996 0 0
|
||||
100 0.36662911 1.1475389 0.24585067 1.0290503 1.1382325 18
|
||||
200 0.73133134 1.0558153 0.49986673 0.73932383 1.049638 34
|
||||
300 1.1229361 1.0218621 0.82641583 0.7589689 1.0205369 40
|
||||
400 1.5826262 0.99541508 1.2201293 0.69171726 0.99190857 52
|
||||
500 1.8834563 0.99351667 1.4778822 1.0147794 1.0005581 63
|
||||
600 2.4225372 0.98954834 1.8740966 1.1362893 0.99760042 61
|
||||
700 3.0172772 0.99153625 2.3351502 1.3284877 0.98731355 39
|
||||
800 3.5307913 1.0012521 2.6477224 1.1404922 0.9846605 52
|
||||
900 3.757064 0.99743944 2.7220653 1.4078087 0.97538456 55
|
||||
1000 4.3165268 1.002214 3.055501 1.2252972 0.99123745 63
|
||||
1100 4.2796945 1.0075233 3.1022956 1.1893685 1.0139864 69
|
||||
1200 4.3719315 1.0037271 3.0054509 1.3886162 1.002661 64
|
||||
1300 4.5628012 0.99368316 3.2690604 1.3621012 0.9810568 56
|
||||
1400 4.6954389 0.99365088 3.1940001 1.8485712 0.99571089 71
|
||||
1500 5.0270163 0.99455258 3.4120396 1.5992539 0.98294263 77
|
||||
1600 5.5897797 1.0021621 3.647347 1.7796904 0.98967622 66
|
||||
1700 5.5330194 1.0130853 3.6407996 1.8005429 1.0068955 62
|
||||
1800 5.3606928 1.0090284 3.5863618 1.3308757 1.0214092 59
|
||||
1900 5.6086195 1.0071865 3.7427101 1.5296314 0.99886937 55
|
||||
2000 5.3726474 1.0064207 3.603621 1.9473142 0.99999816 54
|
||||
2100 5.836183 1.0124553 3.7321841 1.7889397 1.0188986 59
|
||||
2200 5.5090061 1.0113832 3.5884963 1.6617781 1.0071583 59
|
||||
2300 5.4011211 1.0095947 3.520406 1.8937582 0.99689983 61
|
||||
2400 5.2219281 1.0053246 3.3699458 1.7231672 0.99899754 59
|
||||
2500 5.7695275 1.0141459 3.6211469 1.7767598 1.0143133 65
|
||||
2600 5.4206253 1.0182828 3.521774 2.0800518 1.0081603 70
|
||||
2700 5.1401099 1.0085209 3.4200563 2.4019836 1.0107652 59
|
||||
2800 6.5420721 1.0159876 4.1996904 1.863842 1.0160738 61
|
||||
2900 5.9082962 1.0106921 3.7223419 2.0586998 1.0073885 67
|
||||
3000 5.6556123 1.0099021 3.6768976 1.921987 1.0068962 76
|
||||
3100 5.2913762 1.0008567 3.4103831 1.9831969 0.99187526 80
|
||||
3200 5.1032361 0.99756662 3.1967156 2.2448433 0.99743574 93
|
||||
3300 5.2622386 1.0024934 3.3325614 2.0078097 1.0047789 86
|
||||
3400 5.1247527 0.99810102 3.1363556 1.8907269 0.98936508 82
|
||||
3500 4.9424333 1.0009344 3.2153968 1.9002728 0.99161849 71
|
||||
3600 5.1243735 1.0037377 3.3117313 2.1267438 1.0078943 65
|
||||
3700 5.5045819 1.0006119 3.5686193 2.3466538 0.99876164 68
|
||||
3800 5.5355384 1.0022639 3.6701457 2.0383269 1.0008683 76
|
||||
3900 6.4915796 1.0137733 4.3225864 2.6996933 1.0064787 79
|
||||
4000 6.6631737 1.0236248 4.3057163 2.6352666 1.0255232 75
|
||||
4100 6.2999507 1.0263876 4.0101385 2.5479077 1.0168303 79
|
||||
4200 6.7902489 1.0247392 4.4616158 2.4926177 1.0191403 91
|
||||
4300 6.505908 1.0182073 4.0675428 2.168754 1.0177101 74
|
||||
4400 5.9554283 1.0115938 3.5787297 2.9258144 1.0133896 72
|
||||
4500 6.2276609 1.0202416 3.8211204 2.5308249 1.0174385 74
|
||||
4600 6.0485727 1.0195757 3.8217434 2.6421797 1.0201441 78
|
||||
4700 6.511063 1.0220764 3.933486 2.8591093 1.0147269 83
|
||||
4800 6.9478172 1.0106414 4.345402 3.3257663 1.00469 85
|
||||
4900 6.7547045 1.0211842 4.1874576 3.6503845 1.022873 94
|
||||
5000 7.2603949 1.0234313 4.5393985 3.4667806 1.0222306 105
|
||||
5100 7.1899652 1.0256566 4.5421834 3.8137207 1.0317242 99
|
||||
5200 7.1960739 1.026746 4.4288606 3.5523675 1.0242269 97
|
||||
5300 7.1294458 1.017883 4.5799808 3.3917274 1.0145317 99
|
||||
5400 6.2810892 1.0291953 4.0109229 2.8604571 1.0289438 97
|
||||
5500 6.15246 1.0288734 3.8714587 3.2760394 1.0210757 89
|
||||
5600 6.5860526 1.0192882 4.0272883 3.3124298 1.0096258 93
|
||||
5700 7.0296116 1.0097293 4.2652722 3.6049788 1.012463 82
|
||||
5800 6.8372302 1.0140065 4.2205065 4.3686183 1.0088542 93
|
||||
5900 7.8887098 1.0090612 4.9724078 4.457317 1.0045137 92
|
||||
6000 10.120663 1.0312443 6.3025192 4.72018 1.0374722 91
|
||||
6100 9.1318265 1.0304199 5.7084296 4.244548 1.0259056 97
|
||||
6200 8.9758903 1.0295285 5.1842704 4.870955 1.0178851 95
|
||||
6300 9.0088218 1.022484 5.3742805 5.1554352 1.0138365 101
|
||||
6400 10.470322 1.0287848 6.4602103 4.5461489 1.0335978 105
|
||||
6500 11.100779 1.0347405 6.9630121 4.9840664 1.0339044 99
|
||||
6600 10.139333 1.0476079 6.4284839 4.5523893 1.0433517 104
|
||||
6700 8.9706766 1.0386262 5.8387485 4.247024 1.0408151 101
|
||||
6800 7.7799532 1.0362651 4.9946283 4.6093924 1.0274763 102
|
||||
6900 8.0866551 1.0337743 4.9942769 4.1679939 1.0454805 102
|
||||
7000 8.0224277 1.0193598 4.9380527 3.9173115 1.0185001 109
|
||||
7100 7.8361001 1.0211143 4.872673 5.3471479 1.024779 110
|
||||
7200 7.8542147 1.0057183 4.8666653 4.668317 0.99980296 122
|
||||
7300 7.9313852 1.0159181 5.0062527 4.1410294 1.0195705 114
|
||||
7400 7.2769846 1.0155245 4.6349779 4.9138895 1.0005886 119
|
||||
7500 7.5974523 1.0196295 4.7918247 4.2525935 1.0211412 124
|
||||
7600 6.7835063 1.0203187 4.2674694 4.9251624 1.0218296 113
|
||||
7700 6.4039017 1.0119494 4.1086667 5.5240525 1.0078246 118
|
||||
7800 7.0715134 1.0149015 4.2450776 4.8796778 1.0164737 125
|
||||
7900 6.3626535 1.02294 4.202778 4.482164 1.0235878 136
|
||||
8000 6.2423869 1.0212553 4.0460303 5.2753307 1.0124884 132
|
||||
8100 6.550891 1.0223318 4.2993545 5.2634985 1.0163244 143
|
||||
8200 6.9122202 1.008347 4.3551124 5.4108909 1.0084913 142
|
||||
8300 6.9104634 1.0103936 4.4622206 5.6762373 0.99559355 143
|
||||
8400 6.4918879 1.0084381 4.1050732 5.8389788 1.0036021 135
|
||||
8500 7.4377218 1.0216662 4.5229841 5.5431311 1.0260799 123
|
||||
8600 7.572198 1.0228381 4.9058913 7.1028185 1.0015164 116
|
||||
8700 8.204675 1.03457 5.2231696 6.4790244 1.0214635 132
|
||||
8800 8.3118914 1.0381333 5.1795799 6.7437722 1.0290086 132
|
||||
8900 8.2559198 1.0268665 5.218352 7.2191395 1.019804 138
|
||||
9000 8.0403128 1.0339414 4.9310394 6.4942331 1.041527 156
|
||||
9100 7.1773079 1.0397062 4.4993688 7.0272109 1.0388012 167
|
||||
9200 7.1793935 1.0373589 4.3481663 7.4894459 1.0078785 157
|
||||
9300 8.3705146 1.0248112 5.1036971 8.2173072 1.010168 156
|
||||
9400 9.4935002 1.0252907 5.7846951 9.7466018 1.028941 170
|
||||
9500 9.5208037 1.0371093 5.9635099 7.6444933 1.022673 165
|
||||
9600 8.9992217 1.0292895 5.6224192 8.8071452 1.0101362 169
|
||||
9700 8.682661 1.0422224 5.3997636 8.6827834 1.0337928 149
|
||||
9800 7.6191562 1.0350948 4.7198842 8.6125595 1.0300395 151
|
||||
9900 8.0910913 1.0319432 4.8843183 7.9013334 1.0272495 167
|
||||
10000 7.4438347 1.0186098 4.7184985 8.999795 0.99762661 177
|
||||
Loop time of 162.325 on 8 procs for 10000 steps with 16271 atoms
|
||||
|
||||
Performance: 5322.658 tau/day, 61.605 timesteps/s, 1.002 Matom-step/s
|
||||
99.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 33.647 | 64.106 | 79.639 | 169.5 | 39.49
|
||||
Neigh | 0.30808 | 0.44033 | 0.50863 | 9.8 | 0.27
|
||||
Comm | 26.611 | 43.438 | 74.998 | 215.7 | 26.76
|
||||
Output | 0.0072573 | 0.0087791 | 0.0097993 | 0.9 | 0.01
|
||||
Modify | 53.171 | 54.121 | 55.362 | 12.3 | 33.34
|
||||
Other | | 0.2104 | | | 0.13
|
||||
|
||||
Nlocal: 2033.88 ave 2601 max 1413 min
|
||||
Histogram: 1 2 0 0 0 0 2 1 1 1
|
||||
Nghost: 1647.25 ave 1714 max 1617 min
|
||||
Histogram: 4 0 1 0 0 1 1 0 0 1
|
||||
Neighs: 12482.8 ave 17009 max 8679 min
|
||||
Histogram: 1 1 1 0 1 1 2 0 0 1
|
||||
|
||||
Total # of neighbors = 99862
|
||||
Ave neighs/atom = 6.1374224
|
||||
Neighbor list builds = 562
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
Changing box ...
|
||||
triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
|
||||
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
|
||||
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 40000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 2.9202881 0.87320391
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 13 13 13
|
||||
SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
|
||||
SRD per actual grid cell = -2.775698
|
||||
SRD viscosity = -12.180602
|
||||
big/SRD mass density ratio = -5.5653033
|
||||
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
|
||||
# of rescaled SRD velocities = 1
|
||||
ave/max small velocity = 16.14994 40
|
||||
ave/max big velocity = 1.6952661 5.2200074
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.8
|
||||
ghost atom cutoff = 3.8
|
||||
binsize = 13.499745, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tri/lj, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/newton/tri
|
||||
stencil: half/multi/3d/tri
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 106.9 | 107.5 | 107.7 Mbytes
|
||||
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
|
||||
10000 7.4438347 1.0189789 4.7184481 7.9505614 0 0
|
||||
10100 7.0770142 1.0021471 4.4491455 6.606701 1 141
|
||||
10200 6.7628072 1.002308 4.152988 8.5190386 1 125
|
||||
10300 6.5333319 1.0007472 4.1295404 8.2341747 1 109
|
||||
10400 6.3237519 1.0024029 3.8636034 9.4058128 1 95
|
||||
10500 6.6411054 1.0026261 4.2975997 7.6122304 1 82
|
||||
10600 5.7470775 1.0004827 3.7959947 7.3091777 1 67
|
||||
10700 5.9744919 1.0014977 3.6885649 7.5517197 1 59
|
||||
10800 5.8028731 1.0029627 3.7553961 6.2787087 1 49
|
||||
10900 5.3755286 1.0019318 3.5334739 7.1318348 1 41
|
||||
11000 5.3915962 1.001463 3.483172 7.6362496 1 40
|
||||
11100 5.8683672 1.0022459 3.6697589 6.9711866 1 33
|
||||
11200 5.4351801 0.99956703 3.4548447 7.0745257 1 29
|
||||
11300 4.9397513 1.0008287 3.1990325 6.0917337 1 27
|
||||
11400 4.9159845 1.0017862 3.0005677 7.653817 1 26
|
||||
11500 4.9243103 1.0013135 3.1799841 7.744414 1 23
|
||||
11600 5.2036357 1.0017984 3.2963749 7.540477 1 22
|
||||
11700 4.8991892 1.0020757 3.1773032 8.7218471 1 27
|
||||
11800 4.9489399 1.003438 3.1679764 7.1605486 1 26
|
||||
11900 4.82398 1.0019946 3.1939566 7.1397869 1 21
|
||||
12000 4.3531411 1.000532 2.8321416 7.6672501 1 23
|
||||
12100 4.8226081 1.0018898 3.0382137 6.8343432 1 25
|
||||
12200 4.7456418 1.0032116 2.9186038 7.3067818 1 20
|
||||
12300 4.4280468 1.0005857 2.734593 8.0365684 1 22
|
||||
12400 4.7311239 1.0000982 2.8898839 7.9231831 1 22
|
||||
12500 4.7261054 1.0016127 2.9090517 7.6085854 1 24
|
||||
12600 4.7719025 1.0016702 2.9736761 7.6101796 1 26
|
||||
12700 4.386248 1.001394 2.8508378 6.4765102 1 28
|
||||
12800 4.3313538 1.0019737 2.6258221 6.3164681 1 19
|
||||
12900 4.2219861 1.0007469 2.5345699 7.0901077 1 22
|
||||
13000 4.1775643 1.0011891 2.5807017 7.3579938 1 25
|
||||
13100 4.3060837 1.0008671 2.5974066 6.9301328 1 22
|
||||
13200 4.3529062 0.99996469 2.7571632 6.7806287 1 21
|
||||
13300 4.2178709 1.000673 2.7819091 7.6449064 1 18
|
||||
13400 4.2714169 1.0021294 2.7280794 8.0986691 1 18
|
||||
13500 4.3430969 1.0037732 2.6768429 8.1267941 1 18
|
||||
13600 4.3664374 1.0016083 2.6470186 6.2797727 1 20
|
||||
13700 4.4904769 1.0008993 2.7885718 7.7410193 1 22
|
||||
13800 4.2966193 1.001532 2.73862 7.9651302 1 21
|
||||
13900 4.4003185 1.0009984 2.7484129 8.7160439 1 24
|
||||
14000 4.5948292 1.0011748 2.9051777 7.842121 1 22
|
||||
14100 4.6901122 1.0001265 2.9404111 8.9953816 1 20
|
||||
14200 4.8517518 0.99998743 2.9647625 6.6450509 1 22
|
||||
14300 4.889628 1.0018051 3.0891097 7.2671824 1 20
|
||||
14400 4.578862 1.0010629 2.8239776 6.1317183 1 23
|
||||
14500 4.0865406 1.0013917 2.5119661 6.864665 1 19
|
||||
14600 4.30688 1.0009041 2.6817814 6.9007433 1 18
|
||||
14700 4.1295726 1.002342 2.6032093 7.1441648 1 15
|
||||
14800 4.2176021 1.0015157 2.7332903 6.8394683 1 16
|
||||
14900 4.2012664 0.99986345 2.6498409 7.4568241 1 15
|
||||
15000 4.6124269 1.0014751 2.9584178 7.9341875 1 16
|
||||
15100 4.947327 1.0010615 3.0784409 7.6241305 1 21
|
||||
15200 5.253281 1.002095 3.3093754 8.1872718 1 25
|
||||
15300 5.2642369 1.0017799 3.1511136 7.4668389 1 25
|
||||
15400 5.1967916 1.0029407 3.247548 8.0840111 1 23
|
||||
15500 5.7465412 1.001896 3.468834 9.5990471 1 15
|
||||
15600 6.2245772 1.0021086 3.6127689 7.8242016 1 19
|
||||
15700 5.5626191 0.99984979 3.3893723 7.8124588 1 20
|
||||
15800 5.5945727 1.0010291 3.3442448 7.0116922 1 17
|
||||
15900 5.4450219 1.0006248 3.3132381 8.4803413 1 15
|
||||
16000 5.7800459 1.001449 3.5002534 8.7989456 1 19
|
||||
16100 6.1168718 1.0008109 3.8081142 8.0119729 1 18
|
||||
16200 5.4901649 1.0020643 3.3673653 7.3483134 1 17
|
||||
16300 5.4051694 1.0015652 3.3560012 7.4641983 1 19
|
||||
16400 5.4237612 1.0012686 3.3816406 7.3845086 1 14
|
||||
16500 5.1935593 1.001754 3.3340381 7.8607712 1 16
|
||||
16600 5.539343 1.0021073 3.4164309 8.1541097 1 12
|
||||
16700 5.8922923 1.0013792 3.553426 7.5220576 1 14
|
||||
16800 5.956937 1.0005959 3.7630589 8.7417987 1 13
|
||||
16900 5.469721 1.0016219 3.5531223 8.6721994 1 13
|
||||
17000 5.3110154 1.001142 3.4167244 7.4644182 1 15
|
||||
17100 5.9226035 0.99918238 4.0244287 6.5172028 1 16
|
||||
17200 5.4897042 0.99981565 3.4350691 5.6840394 1 20
|
||||
17300 5.4302636 1.0021571 3.421473 6.4317025 1 21
|
||||
17400 5.5559131 1.0013807 3.4951403 6.874191 1 24
|
||||
17500 5.4068006 1.0010448 3.4506835 7.7069504 1 22
|
||||
17600 4.9283792 1.0007628 3.1736308 7.3098058 1 20
|
||||
17700 4.9319722 0.99935896 3.0956257 8.2120111 1 15
|
||||
17800 4.6842391 1.00037 2.9602433 7.4116352 1 17
|
||||
17900 4.7714682 1.0009332 2.9666778 7.5925131 1 17
|
||||
18000 4.7233188 1.0035687 3.0991778 7.1636357 1 10
|
||||
18100 4.6487958 1.0020255 3.10781 6.8468658 1 12
|
||||
18200 4.6284129 1.0012617 3.089724 6.3082275 1 13
|
||||
18300 4.7136404 0.99962415 3.1261978 7.3359556 1 15
|
||||
18400 5.0367681 1.0011016 3.2413493 8.3910633 1 14
|
||||
18500 4.9658104 1.0025407 3.2420827 7.4701216 1 17
|
||||
18600 4.6100059 1.0014508 3.0216884 6.553483 1 17
|
||||
18700 4.3246452 1.0016721 2.7810363 6.7450293 1 19
|
||||
18800 4.9415788 1.0012406 3.1661907 7.5544034 1 18
|
||||
18900 5.3930915 1.000138 3.2557456 7.350955 1 21
|
||||
19000 5.1938599 1.0007364 3.2398733 6.5397956 1 22
|
||||
19100 5.4433048 1.0019191 3.2699245 8.3625772 1 22
|
||||
19200 6.1303261 1.0004005 3.7823203 8.0537369 1 22
|
||||
19300 5.5762518 1.0008117 3.5689121 8.3714373 1 22
|
||||
19400 5.1316743 0.9999834 3.099381 7.405287 1 23
|
||||
19500 5.2064799 1.0012007 3.3059455 7.3499127 1 25
|
||||
19600 5.1650099 1.0023314 3.3759492 7.3637616 1 21
|
||||
19700 5.8316278 1.0023317 3.601564 7.153887 1 19
|
||||
19800 5.6435147 1.0010657 3.4967581 6.8899334 1 21
|
||||
19900 5.4071193 0.99961357 3.4977894 6.1068438 1 20
|
||||
20000 5.5058495 1.000982 3.5185057 8.5657603 1 19
|
||||
20100 5.6551271 1.0025852 3.5672369 7.8242273 1 20
|
||||
20200 5.7196886 1.002283 3.6010925 7.1449072 1 22
|
||||
20300 5.5593553 1.0009987 3.4363398 8.4141755 1 21
|
||||
20400 5.5550247 1.001081 3.3950874 8.0222131 1 20
|
||||
20500 5.4510415 0.99997273 3.5505093 7.5243655 1 18
|
||||
20600 5.8014064 1.0007611 3.8084579 7.6583499 1 18
|
||||
20700 5.7337315 1.0020309 3.7973684 8.7376766 1 17
|
||||
20800 5.2512898 0.99901254 3.5027763 7.8902791 1 14
|
||||
20900 5.3245034 1.0014504 3.3354615 6.7030716 1 17
|
||||
21000 5.2071731 1.0020459 3.3881369 5.8616999 1 20
|
||||
21100 5.3187535 1.0010762 3.2845672 8.1422146 1 21
|
||||
21200 5.5298545 0.99942313 3.4393978 7.1183144 1 22
|
||||
21300 5.8430744 1.0008652 3.719408 7.8522038 1 20
|
||||
21400 5.8190457 1.0017046 3.5624252 7.8150165 1 20
|
||||
21500 6.004585 1.0035276 3.9161914 7.7719377 1 21
|
||||
21600 6.7202635 0.99970072 3.9642141 8.7934294 1 18
|
||||
21700 6.8590346 1.0007883 4.4285217 8.9014638 1 20
|
||||
21800 6.627638 1.0012117 4.1154082 8.3153026 1 22
|
||||
21900 7.8281047 1.0008299 4.8842343 8.4016227 1 20
|
||||
22000 7.200038 1.0014681 4.4141419 9.4091956 1 18
|
||||
22100 7.7442011 1.0018051 4.7850371 8.9885489 1 15
|
||||
22200 7.4770203 1.0033558 4.7512643 8.4898148 1 17
|
||||
22300 8.1080801 1.0000019 5.2725185 9.2314625 1 14
|
||||
22400 7.8068311 1.0020672 4.9055683 8.4064748 1 12
|
||||
22500 7.4594636 1.0008427 4.6586396 8.5102986 1 11
|
||||
22600 6.9380609 1.0024634 4.2435619 10.395118 1 16
|
||||
22700 6.9338066 1.001056 4.3436179 7.9126284 1 18
|
||||
22800 6.8049493 1.0020052 4.1443407 7.8228868 1 18
|
||||
22900 6.2280158 1.0021474 3.7695343 7.3179647 1 20
|
||||
23000 5.649403 1.0017128 3.5941976 7.2964709 1 19
|
||||
23100 5.3203116 1.001912 3.3807399 6.6454551 1 15
|
||||
23200 5.8172882 1.0005742 3.6625896 8.4256312 1 15
|
||||
23300 5.9647182 1.0015466 3.9106019 8.3303303 1 14
|
||||
23400 5.9784055 1.0034542 3.7229235 7.7934273 1 14
|
||||
23500 5.377627 1.00192 3.5481778 6.8195124 1 17
|
||||
23600 5.4807136 1.0014662 3.563123 7.6356376 1 18
|
||||
23700 5.8896329 1.0013553 3.7990694 8.5513408 1 13
|
||||
23800 6.3463707 0.9999403 3.9609397 8.5741923 1 11
|
||||
23900 6.656669 1.0014998 4.1993183 9.0862996 1 13
|
||||
24000 7.583723 1.0025057 4.7628652 7.5007245 1 20
|
||||
24100 6.9868359 1.0014089 4.4369841 7.692833 1 25
|
||||
24200 7.1966062 1.0013149 4.4384528 9.5264821 1 18
|
||||
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|
||||
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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42800 13.240256 1.0027899 8.2014429 10.506497 1 32
|
||||
42900 12.784336 1.0001406 8.0823431 12.258209 1 33
|
||||
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|
||||
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|
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43200 12.669284 1.0018944 7.8511966 10.580104 1 32
|
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43300 13.155032 1.001144 8.0337768 10.6652 1 39
|
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43400 12.155928 1.0019472 7.5886584 11.234772 1 35
|
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|
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|
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|
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46600 7.2261291 1.0005569 4.4751221 6.5847138 1 27
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|
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|
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|
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|
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48500 8.3752816 1.001333 5.1071228 8.2267308 1 32
|
||||
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|
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|
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|
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|
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49400 8.2628465 1.0010877 5.2292977 8.0196533 1 27
|
||||
49500 8.1436558 1.0015175 5.0344712 8.0712037 1 30
|
||||
49600 8.5182498 1.0021589 5.1029028 8.6869789 1 28
|
||||
49700 8.3604444 1.0015016 5.0333696 9.4861656 1 25
|
||||
49800 7.336335 1.0020055 4.6365173 8.7210022 1 30
|
||||
49900 7.432996 1.0016415 4.7090587 8.7033033 1 29
|
||||
50000 7.4937053 1.001014 4.7212573 9.0890363 1 29
|
||||
Loop time of 999.576 on 8 procs for 40000 steps with 16271 atoms
|
||||
|
||||
Performance: 3457.466 tau/day, 40.017 timesteps/s, 651.116 katom-step/s
|
||||
99.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 293.48 | 403.7 | 545.29 | 357.5 | 40.39
|
||||
Neigh | 2.4176 | 3.2721 | 3.8303 | 25.2 | 0.33
|
||||
Comm | 163.58 | 305.88 | 419.83 | 416.7 | 30.60
|
||||
Output | 0.032483 | 0.034794 | 0.040514 | 1.2 | 0.00
|
||||
Modify | 281.15 | 285.67 | 293.8 | 24.3 | 28.58
|
||||
Other | | 1.023 | | | 0.10
|
||||
|
||||
Nlocal: 2033.88 ave 2657 max 1198 min
|
||||
Histogram: 2 0 0 0 0 2 1 0 1 2
|
||||
Nghost: 1628.12 ave 1719 max 1569 min
|
||||
Histogram: 2 0 1 1 2 1 0 0 0 1
|
||||
Neighs: 13566 ave 18212 max 8488 min
|
||||
Histogram: 1 0 0 1 2 1 2 0 0 1
|
||||
|
||||
Total # of neighbors = 108528
|
||||
Ave neighs/atom = 6.6700264
|
||||
Neighbor list builds = 2447
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:19:22
|
||||
343
examples/ASPHERE/tri/log.1Feb24.tri.srd.g++.1
Normal file
343
examples/ASPHERE/tri/log.1Feb24.tri.srd.g++.1
Normal file
@ -0,0 +1,343 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
|
||||
|
||||
units lj
|
||||
atom_style tri
|
||||
atom_modify first big map yes
|
||||
|
||||
read_data data.tri.srd
|
||||
Reading data file ...
|
||||
orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1500 atoms
|
||||
1500 triangles
|
||||
read_data CPU = 0.013 seconds
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block INF INF INF INF INF INF
|
||||
lattice sc 20.0
|
||||
Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
|
||||
create_atoms 2 region box
|
||||
Created 91125 atoms
|
||||
using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
|
||||
create_atoms CPU = 0.014 seconds
|
||||
|
||||
group big type 1
|
||||
1500 atoms in group big
|
||||
group small type 2
|
||||
91125 atoms in group small
|
||||
set group small mass 0.01
|
||||
Setting atom values ...
|
||||
91125 settings made for mass
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.8
|
||||
ghost atom cutoff = 1.8
|
||||
binsize = 0.9, bins = 19 19 19
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 76354 atoms, new total = 16271
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule/intra big include big
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style tri/lj 3.5
|
||||
pair_coeff 1 1 0.1 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
|
||||
create bodies CPU = 0.000 seconds
|
||||
125 rigid bodies with 1500 atoms
|
||||
1.8601881 = max distance from body owner to body atom
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
|
||||
|
||||
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute_modify tbig extra/dof -4500
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
|
||||
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
|
||||
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
|
||||
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
|
||||
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 2.9202881 0.87320391
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 17 17 17
|
||||
SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
|
||||
SRD per actual grid cell = -3.9971745
|
||||
SRD viscosity = -34.162587
|
||||
big/SRD mass density ratio = -3.3753691
|
||||
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 19.970837 35.150443
|
||||
ave/max big velocity = 0 0
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.8
|
||||
ghost atom cutoff = 3.8
|
||||
binsize = 16.874681, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tri/lj, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/3d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 381.8 | 381.8 | 381.8 Mbytes
|
||||
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
|
||||
0 0 1.4502537 0 -0.15976045 0 0
|
||||
100 0.41802172 1.152223 0.27557714 1.0421065 1.1470081 283
|
||||
200 0.79710339 1.0669332 0.5813323 0.97699684 1.0361619 534
|
||||
300 1.3739181 1.0275476 1.0869716 0.81001536 1.0211312 658
|
||||
400 1.9355117 1.0155457 1.5813236 1.7798798 0.99354559 831
|
||||
500 2.8557382 1.0005021 2.267698 3.3903849 0.98597972 927
|
||||
600 4.7851916 1.0156689 3.730334 2.838776 0.99140534 1053
|
||||
700 5.3647697 1.0176657 3.9593121 5.1189107 0.9972029 1218
|
||||
800 8.23688 1.0268086 5.899689 6.8199153 0.99310516 1349
|
||||
900 9.9330758 1.0356047 7.0260595 7.2596589 0.98360014 1607
|
||||
1000 9.8719995 1.043178 6.9903792 10.05101 1.0045416 1805
|
||||
Loop time of 79.2664 on 1 procs for 1000 steps with 16271 atoms
|
||||
|
||||
Performance: 1089.995 tau/day, 12.616 timesteps/s, 205.270 katom-step/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 | 57.961 | 57.961 | 57.961 | 0.0 | 73.12
|
||||
Neigh | 0.34589 | 0.34589 | 0.34589 | 0.0 | 0.44
|
||||
Comm | 0.28615 | 0.28615 | 0.28615 | 0.0 | 0.36
|
||||
Output | 0.0022784 | 0.0022784 | 0.0022784 | 0.0 | 0.00
|
||||
Modify | 20.644 | 20.644 | 20.644 | 0.0 | 26.04
|
||||
Other | | 0.02724 | | | 0.03
|
||||
|
||||
Nlocal: 16271 ave 16271 max 16271 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4612 ave 4612 max 4612 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 99463 ave 99463 max 99463 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 99463
|
||||
Ave neighs/atom = 6.1129003
|
||||
Neighbor list builds = 72
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
Changing box ...
|
||||
triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
|
||||
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
|
||||
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 2000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 2.9202881 0.87320391
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 13 13 13
|
||||
SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
|
||||
SRD per actual grid cell = -2.775698
|
||||
SRD viscosity = -12.180602
|
||||
big/SRD mass density ratio = -5.5653033
|
||||
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
|
||||
# of rescaled SRD velocities = 3
|
||||
ave/max small velocity = 16.23763 40
|
||||
ave/max big velocity = 1.9825234 5.257255
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.8
|
||||
ghost atom cutoff = 3.8
|
||||
binsize = 13.499745, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tri/lj, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton/tri
|
||||
stencil: half/multi/3d/tri
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 278.4 | 278.4 | 278.4 Mbytes
|
||||
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
|
||||
1000 9.8719995 1.0317167 6.98982 4.0948969 0 0
|
||||
1100 7.6460335 1.0028444 5.2446585 6.6348814 1 1320
|
||||
1200 6.2789381 1.0012003 4.5257435 6.3278972 1 1024
|
||||
1300 5.5060209 1.002182 3.7063549 7.0004503 1 794
|
||||
1400 5.4107119 1.002291 3.594515 7.9511695 1 621
|
||||
1500 5.072582 1.0001037 3.2501353 8.6993671 1 503
|
||||
1600 4.7912016 0.99982803 3.1208274 6.464157 1 416
|
||||
1700 4.5518848 1.0030059 2.9084074 6.3278992 1 346
|
||||
1800 4.368682 1.000831 2.807184 6.7382017 1 282
|
||||
1900 4.458655 1.0012568 2.7966515 6.0124309 1 246
|
||||
2000 4.1256128 1.0004032 2.763649 6.3707442 1 208
|
||||
2100 3.7040346 1.0004125 2.4398152 5.4213931 1 181
|
||||
2200 4.2347861 1.002625 2.6206986 6.6832437 1 151
|
||||
2300 4.254984 1.0028871 2.6794167 7.1661525 1 127
|
||||
2400 4.1017692 1.0028508 2.6371178 8.388599 1 105
|
||||
2500 3.9285571 1.0002888 2.5002741 6.0806187 1 95
|
||||
2600 3.6239964 1.0012152 2.2573993 6.7863124 1 80
|
||||
2700 3.4085702 1.0023974 2.1179914 6.7351139 1 68
|
||||
2800 3.1399303 1.0005349 2.0163219 6.4502765 1 61
|
||||
2900 3.1277562 1.0004013 2.0453134 6.6485498 1 51
|
||||
3000 3.0737732 1.0022962 1.997382 6.797214 1 44
|
||||
Loop time of 206.387 on 1 procs for 2000 steps with 16271 atoms
|
||||
|
||||
Performance: 837.264 tau/day, 9.691 timesteps/s, 157.675 katom-step/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 | 173.6 | 173.6 | 173.6 | 0.0 | 84.12
|
||||
Neigh | 1.0077 | 1.0077 | 1.0077 | 0.0 | 0.49
|
||||
Comm | 0.58656 | 0.58656 | 0.58656 | 0.0 | 0.28
|
||||
Output | 0.0042824 | 0.0042824 | 0.0042824 | 0.0 | 0.00
|
||||
Modify | 31.128 | 31.128 | 31.128 | 0.0 | 15.08
|
||||
Other | | 0.05664 | | | 0.03
|
||||
|
||||
Nlocal: 16271 ave 16271 max 16271 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4521 ave 4521 max 4521 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 94777 ave 94777 max 94777 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 94777
|
||||
Ave neighs/atom = 5.8249032
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:04:47
|
||||
343
examples/ASPHERE/tri/log.1Feb24.tri.srd.g++.4
Normal file
343
examples/ASPHERE/tri/log.1Feb24.tri.srd.g++.4
Normal file
@ -0,0 +1,343 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
|
||||
|
||||
units lj
|
||||
atom_style tri
|
||||
atom_modify first big map yes
|
||||
|
||||
read_data data.tri.srd
|
||||
Reading data file ...
|
||||
orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1500 atoms
|
||||
1500 triangles
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block INF INF INF INF INF INF
|
||||
lattice sc 20.0
|
||||
Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
|
||||
create_atoms 2 region box
|
||||
Created 91125 atoms
|
||||
using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
|
||||
create_atoms CPU = 0.005 seconds
|
||||
|
||||
group big type 1
|
||||
1500 atoms in group big
|
||||
group small type 2
|
||||
91125 atoms in group small
|
||||
set group small mass 0.01
|
||||
Setting atom values ...
|
||||
91125 settings made for mass
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
System init for delete_atoms ...
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.8
|
||||
ghost atom cutoff = 1.8
|
||||
binsize = 0.9, bins = 19 19 19
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command delete_atoms, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
|
||||
Deleted 76354 atoms, new total = 16271
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule/intra big include big
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style tri/lj 3.5
|
||||
pair_coeff 1 1 0.1 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
|
||||
create bodies CPU = 0.000 seconds
|
||||
125 rigid bodies with 1500 atoms
|
||||
1.8601881 = max distance from body owner to body atom
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
|
||||
|
||||
fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute_modify tbig extra/dof -4500
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
|
||||
|
||||
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
|
||||
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
|
||||
|
||||
run 1000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
|
||||
|
||||
@Article{Intveld08,
|
||||
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
|
||||
title = {Accurate and Efficient Methods for Modeling Colloidal
|
||||
Mixtures in an Explicit Solvent using Molecular Dynamics},
|
||||
journal = {Comput.\ Phys.\ Commut.},
|
||||
year = 2008,
|
||||
volume = 179,
|
||||
pages = {320--329}
|
||||
}
|
||||
|
||||
@article{Shire2020,
|
||||
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
|
||||
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
|
||||
Detection Applied to Investigate the Quasi-Static Limit},
|
||||
journal = {Computational Particle Mechanics},
|
||||
year = {2020}
|
||||
@article{Monti2022,
|
||||
author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
|
||||
Ishan and Silbert, Leonardo E. and Grest, Gary S.
|
||||
and Lechman, Jeremy B.},
|
||||
title = {Large-scale frictionless jamming with power-law particle
|
||||
size distributions},
|
||||
journal = {Phys. Rev. E},
|
||||
volume = {106}
|
||||
issue = {3}
|
||||
year = {2022}
|
||||
}
|
||||
|
||||
- fix srd command: doi:10.1063/1.3419070
|
||||
|
||||
@Article{Petersen10,
|
||||
author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
|
||||
G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
|
||||
title = {Mesoscale Hydrodynamics via Stochastic Rotation
|
||||
Dynamics: Comparison with {L}ennard-{J}ones Fluid},
|
||||
journal = {J.~Chem.\ Phys.},
|
||||
year = 2010,
|
||||
volume = 132,
|
||||
pages = 174106
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
|
||||
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 2.9202881 0.87320391
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 17 17 17
|
||||
SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
|
||||
SRD per actual grid cell = -3.9971745
|
||||
SRD viscosity = -34.162587
|
||||
big/SRD mass density ratio = -3.3753691
|
||||
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 19.970837 35.150443
|
||||
ave/max big velocity = 0 0
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.8
|
||||
ghost atom cutoff = 3.8
|
||||
binsize = 16.874681, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tri/lj, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton
|
||||
stencil: half/multi/3d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 184.3 | 184.9 | 185.4 Mbytes
|
||||
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
|
||||
0 0 1.4502537 0 -0.15949051 0 0
|
||||
100 0.39689465 1.1495173 0.26931663 1.0004927 1.1170389 279
|
||||
200 0.82155086 1.0684809 0.60689485 0.81307973 1.0433122 467
|
||||
300 1.3210872 1.0334277 1.0368935 1.0853416 0.99443391 621
|
||||
400 1.9755695 1.0149146 1.6438403 1.7258285 0.9925525 788
|
||||
500 3.0111365 1.0121291 2.4285289 2.5210058 0.99688885 922
|
||||
600 4.5413799 1.014305 3.4727946 3.8290233 0.99002027 1063
|
||||
700 6.6071849 1.0062952 4.9025772 3.9595327 0.99573591 1186
|
||||
800 7.6256618 1.0151252 5.3662442 5.0088255 0.99640985 1371
|
||||
900 8.1578206 1.0148959 5.7716683 6.6059298 0.96053165 1555
|
||||
1000 10.749617 1.0282309 7.6209538 11.277602 1.0012602 1844
|
||||
Loop time of 28.4136 on 4 procs for 1000 steps with 16271 atoms
|
||||
|
||||
Performance: 3040.793 tau/day, 35.194 timesteps/s, 572.647 katom-step/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 12.454 | 15.242 | 17.781 | 48.4 | 53.64
|
||||
Neigh | 0.093078 | 0.094516 | 0.097759 | 0.6 | 0.33
|
||||
Comm | 0.48732 | 2.9927 | 5.7363 | 107.5 | 10.53
|
||||
Output | 0.00080706 | 0.0008431 | 0.00086933 | 0.0 | 0.00
|
||||
Modify | 10.015 | 10.063 | 10.111 | 1.4 | 35.42
|
||||
Other | | 0.02046 | | | 0.07
|
||||
|
||||
Nlocal: 4067.75 ave 4467 max 3606 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 2313.5 ave 2327 max 2296 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 24883 ave 26066 max 24145 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 99532
|
||||
Ave neighs/atom = 6.1171409
|
||||
Neighbor list builds = 70
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
Changing box ...
|
||||
triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
|
||||
|
||||
fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
|
||||
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 2000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 2.9202881 0.87320391
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 13 13 13
|
||||
SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
|
||||
SRD per actual grid cell = -2.775698
|
||||
SRD viscosity = -12.180602
|
||||
big/SRD mass density ratio = -5.5653033
|
||||
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
|
||||
# of rescaled SRD velocities = 3
|
||||
ave/max small velocity = 16.10299 40
|
||||
ave/max big velocity = 2.0311414 11.34118
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.8
|
||||
ghost atom cutoff = 3.8
|
||||
binsize = 13.499745, bins = 1 1 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tri/lj, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/atomonly/newton/tri
|
||||
stencil: half/multi/3d/tri
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 148.8 | 149.5 | 150 Mbytes
|
||||
Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
|
||||
1000 10.749616 1.0167438 7.6203704 5.4893075 0 0
|
||||
1100 9.0727748 1.003438 6.1822573 8.6707036 1 1339
|
||||
1200 7.1960998 1.0003968 4.8077632 6.7809972 1 1039
|
||||
1300 6.2680889 1.0011134 4.3139658 8.2260362 1 861
|
||||
1400 5.8199503 1.0024475 3.9876867 7.0322957 1 692
|
||||
1500 5.399935 0.99757802 3.4552534 7.905565 1 577
|
||||
1600 5.0830248 1.0023727 3.1330433 7.6897887 1 479
|
||||
1700 4.8728937 1.0027203 3.0838267 7.606406 1 389
|
||||
1800 4.8443541 1.0018057 3.115321 7.4547572 1 317
|
||||
1900 5.0622362 1.0007126 2.9336473 6.514338 1 268
|
||||
2000 5.022699 1.0030275 3.1244763 7.2999286 1 223
|
||||
2100 4.4605894 1.0019457 2.9262733 8.3475145 1 196
|
||||
2200 4.6544992 1.0023701 3.0140329 7.3670747 1 164
|
||||
2300 4.1954825 1.0012089 2.5802739 7.5553707 1 142
|
||||
2400 4.0806819 1.0000292 2.6492187 7.5648723 1 122
|
||||
2500 3.7437189 0.99949605 2.3660722 8.2155316 1 104
|
||||
2600 4.2333926 1.0002823 2.5704515 7.2839635 1 106
|
||||
2700 3.7542455 1.001394 2.4146222 6.3785983 1 86
|
||||
2800 3.4011329 0.99832028 2.141193 6.3869497 1 78
|
||||
2900 3.4579019 1.0007319 2.1839274 6.241817 1 64
|
||||
3000 3.6128019 1.0017345 2.2982426 5.8975992 1 55
|
||||
Loop time of 67.0194 on 4 procs for 2000 steps with 16271 atoms
|
||||
|
||||
Performance: 2578.358 tau/day, 29.842 timesteps/s, 485.561 katom-step/s
|
||||
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 36.774 | 43.583 | 50.126 | 71.5 | 65.03
|
||||
Neigh | 0.29299 | 0.3134 | 0.32399 | 2.2 | 0.47
|
||||
Comm | 0.75102 | 7.2688 | 14.075 | 174.8 | 10.85
|
||||
Output | 0.0016347 | 0.0017229 | 0.0018802 | 0.2 | 0.00
|
||||
Modify | 15.794 | 15.808 | 15.828 | 0.3 | 23.59
|
||||
Other | | 0.04379 | | | 0.07
|
||||
|
||||
Nlocal: 4067.75 ave 4560 max 3583 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 2256.75 ave 2292 max 2241 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 23706 ave 24669 max 22450 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
|
||||
Total # of neighbors = 94824
|
||||
Ave neighs/atom = 5.8277918
|
||||
Neighbor list builds = 108
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:36
|
||||
Reference in New Issue
Block a user