Environment: CentOS Linux 7 (Core)
LAMMPS version: LAMMPS-15Sep2022
Packages:
make yes-mc yes-molecule yes-asphere yes-peri yes-sph yes-EXTRA-PAIR
make serial
with fluid membrane package from: https://data.mendeley.com/datasets/4v53nkv5hc/1
(code modified to match 2022 version)
Input file: (A modification based on Ballistic impact response of lipid membranes - Nanoscale (RSC Publishing))
# This is LAMMPS input script specifies a CG model of curli fiber and self-assemble
units lj
atom_style hybrid molecular ellipsoid
boundary p p p
# create simulation box
region box block 0 400 0 400 0 400 units box
create_box 2 box
lattice diamond 1.0
region 1 sphere 200 200 215 10 side in units box
create_atoms 2 region 1 units box
region 3 block 0 400 0 400 200 201 side in units box
lattice diamond 1.0
create_atoms 1 region 3 units box
group memberane type 1
group bullet type 2
pair_style hybrid lj/cut 2.5 harmonic/cut fluidmembrane 2.6
pair_coeff 2 2 lj/cut 0.0 1.0 # bullet-bullet
pair_coeff 1 2 harmonic/cut 0.5 2.5 # bullet-membrane
pair_coeff 1 1 fluidmembrane 1.0 1.0 2.6 4 3 0.0
# create initial velocities
velocity memberane create 0.2 4928459 dist gaussian
# change neighbor list parameters to avoid dangerous builds
neighbor 0.3 bin
neigh_modify every 8 delay 0
# specify simulation parameters
timestep 0.001
thermo 200
thermo_style custom step temp pe etotal pxx pyy pzz pxy pxz pyz lx ly lz
dump 2 all atom 6000 Bullet.lammpstrj
fix 2 memberane nve/asphere
fix 3 memberane temp/berendsen 0.2 0.2 1.0
fix 4 memberane press/berendsen x 0.0 0.0 1.0 y 0.0 0.0 1.0 couple xy dilate partial
run 30000
unfix 4
unfix 3
unfix 2
region hole cylinder z 200 200 195 190 210 side in units box
group inside region hole
group outside subtract memberane inside
group InsideMem subtract memberane outside
fix 5 outside setforce 0.0 0.0 0.0
velocity outside set 0.0 0.0 0.0 units box
fix 7 InsideMem nve/asphere
fix 8 InsideMem temp/berendsen 0.2 0.2 1.0
velocity bullet set 0.0 0.0 -0.65 units box
fix 1 bullet rigid single # fix bullet as a single regid particle.
compute 1 bullet com
compute 2 all ke
compute 3 all pe
compute 4 bullet ke
compute 5 memberane group/group bullet
fix 11 all ave/time 1 10 200 c_1[3] c_2 c_3 c_4 file Velocity_r10_v0_65.txt
fix 12 all ave/time 1 10 200 c_1[3] c_5 c_5[3] file force_r10_v0_65.txt
run 800000
#pair_write 1 2 500 r 0.8 3.0 table_LJrep126.txt LJrep126
write_restart bullet.restart
Yet I got the following error message:
LAMMPS (15 Sep 2022)
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:133)
Created orthogonal box = (0 0 0) to (400 400 400)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 2 2 2
Created 4158 atoms
using box units in orthogonal box = (0 0 0) to (400 400 400)
create_atoms CPU = 0.005 seconds
Lattice spacing in x,y,z = 2 2 2
Created 240000 atoms
using box units in orthogonal box = (0 0 0) to (400 400 400)
create_atoms CPU = 0.117 seconds
240000 atoms in group memberane
4158 atoms in group bullet
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair fluidmembrane command:
The log file lists these citations in BibTeX format.
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
ERROR on proc 0: Fix nve/asphere requires extended particles (../fix_nve_asphere.cpp:54)
Last command: run 30000
The particles I created is an ellipsoid already, but I don’t know how to make them “extended particles”. Sorry if this is a super-basic question, and thank you in advance!
