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Added bd integrator for ellipsoidal particles as well.

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This commit is contained in:
Sam Cameron
2020-12-16 16:14:13 +00:00
parent 86ebe0a9d3
commit f2e7f5263e
9 changed files with 876 additions and 2 deletions
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2
examples/USER/misc/bd_asphere/README.txt Normal file
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The input file in2d.bd demonstrates how to run a 2d simulation
of ellipsoidal particles undergoing overdamped brownian motion.

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examples/USER/misc/bd_asphere/in3d.bd Normal file
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# 3d overdamped brownian dynamics
variable rng string gaussian
variable gamma_t equal 4.0
variable gamma_r equal 1.0
variable D_t equal 7.0
variable D_r equal 13.0
variable seed equal 1974019
variable params string ${rng}_${gamma_t}_${gamma_r}_${D_t}_${D_r}
log log_${params}_3d.lammps.log
units lj
atom_style hybrid dipole sphere ellipsoid
dimension 3
newton off
lattice sc 0.4
region box block -4 4 -4 4 -4 4
create_box 1 box
create_atoms 1 box
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * shape 1 1 1
set type * quat/random ${seed}
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all bd/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 50000
run 50000
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step temp epair c_msd[*] c_press
# write trajectory and thermo in a log-scale frequency
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
# x y xu yu mux muy muz fx fy fz
#dump_modify 1 first yes sort id
timestep 0.00001
thermo 10000
# main run
run 120000

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examples/USER/misc/bd_asphere/log_gaussian_4_1_7_13_3d.lammps.log Normal file
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units lj
atom_style hybrid dipole sphere ellipsoid
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157)
WARNING: Peratom rmass is in multiple sub-styles - must be used consistently (src/atom_vec_hybrid.cpp:219)
dimension 3
newton off
lattice sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region box block -4 4 -4 4 -4 4
create_box 1 box
Created orthogonal box = (-5.4288352 -5.4288352 -5.4288352) to (5.4288352 5.4288352 5.4288352)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
create_atoms CPU = 0.001 seconds
mass * 1.0
set type * dipole/random ${seed} 1.0
set type * dipole/random 1974019 1.0
Setting atom values ...
512 settings made for dipole/random
set type * shape 1 1 1
Setting atom values ...
512 settings made for shape
set type * quat/random ${seed}
set type * quat/random 1974019
Setting atom values ...
512 settings made for quat/random
velocity all create 1.0 1 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 1 check yes
pair_style none
fix 1 all bd/asphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole
fix 1 all bd/asphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} dipole
fix 1 all bd/asphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} dipole
fix 1 all bd/asphere 4 1 7 ${D_r} ${seed} rng ${rng} dipole
fix 1 all bd/asphere 4 1 7 13 ${seed} rng ${rng} dipole
fix 1 all bd/asphere 4 1 7 13 1974019 rng ${rng} dipole
fix 1 all bd/asphere 4 1 7 13 1974019 rng gaussian dipole
compute press all pressure NULL virial
thermo_style custom step temp epair c_press
#equilibration
timestep 0.0000000001
thermo 50000
run 50000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.379 | 5.379 Mbytes
Step Temp E_pair c_press
0 1 0 0
50000 1.3923773e+11 0 0
Loop time of 5.68636 on 1 procs for 50000 steps with 512 atoms
Performance: 0.076 tau/day, 8792.977 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.11589 | 0.11589 | 0.11589 | 0.0 | 2.04
Output | 2.1155e-05 | 2.1155e-05 | 2.1155e-05 | 0.0 | 0.00
Modify | 5.4911 | 5.4911 | 5.4911 | 0.0 | 96.57
Other | | 0.07936 | | | 1.40
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 217.000 ave 217 max 217 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
#initialisation for the main run
# MSD
compute msd all msd
thermo_style custom step temp epair c_msd[*] c_press
# write trajectory and thermo in a log-scale frequency
dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz
dump 1 all custom 1000 dump_gaussian_4_1_7_13_2d.lammpstrj id type x y xu yu mux muy muz fx fy fz
dump_modify 1 first yes sort id
timestep 0.00001
thermo 10000
# main run
run 120000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 7.103 | 7.103 | 7.103 Mbytes
Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
0 1.3923773e+11 0 0 0 0 0 0
10000 1413805.2 0 1.3943053 1.4055827 1.4346505 4.2345385 0
20000 1380788.4 0 2.8560158 2.6537192 2.698195 8.2079299 0
30000 1368735.7 0 4.2694087 4.1286924 3.9635117 12.361613 0
40000 1349446 0 5.4328386 6.0271243 5.3571941 16.817157 0
50000 1366690 0 7.0372792 7.3342977 6.7676981 21.139275 0
60000 1413212.4 0 8.6092241 8.3859529 8.3650987 25.360276 0
70000 1401310 0 10.085131 9.4972009 9.7949174 29.377249 0
80000 1419160.7 0 11.413946 10.964643 11.007284 33.385873 0
90000 1298713.5 0 12.556318 12.457196 12.055966 37.06948 0
100000 1430838.3 0 14.104796 13.817001 13.596538 41.518335 0
110000 1364246.8 0 15.382464 15.09201 15.017312 45.491785 0
120000 1389237.6 0 16.632972 16.343173 16.015748 48.991892 0
Loop time of 13.595 on 1 procs for 120000 steps with 512 atoms
Performance: 7626.329 tau/day, 8826.770 timesteps/s
100.0% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0.00079148 | 0.00079148 | 0.00079148 | 0.0 | 0.01
Comm | 0.029132 | 0.029132 | 0.029132 | 0.0 | 0.21
Output | 0.15178 | 0.15178 | 0.15178 | 0.0 | 1.12
Modify | 13.222 | 13.222 | 13.222 | 0.0 | 97.25
Other | | 0.1916 | | | 1.41
Nlocal: 512.000 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 1110
Dangerous builds = 0
Total wall time: 0:00:19