161 lines
6.1 KiB
Groff
161 lines
6.1 KiB
Groff
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-106-g5d02e140d4)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# flat membrane demo
|
|
variable r0 equal 0.97
|
|
variable d1 equal ${r0}
|
|
variable d1 equal 0.97
|
|
variable d2 equal sqrt(3.0)*${r0}
|
|
variable d2 equal sqrt(3.0)*0.97
|
|
variable d3 equal 3.0*${r0}
|
|
variable d3 equal 3.0*0.97
|
|
variable ro equal 2./${d1}/${d2}/${d3}
|
|
variable ro equal 2./0.97/${d2}/${d3}
|
|
variable ro equal 2./0.97/1.68008928334181/${d3}
|
|
variable ro equal 2./0.97/1.68008928334181/2.91
|
|
|
|
variable T equal 0.23
|
|
variable LD equal 1.0
|
|
|
|
units lj
|
|
atom_style ellipsoid
|
|
|
|
boundary p p p
|
|
|
|
lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
|
lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
|
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
|
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
|
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
|
|
Lattice spacing in x,y,z = 0.97 1.6800893 2.91
|
|
|
|
|
|
region box block 0 40 0 24 -20 20
|
|
create_box 1 box
|
|
Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
|
|
1 by 1 by 1 MPI processor grid
|
|
region membrane block 0 40 0 24 -0.5 0.5
|
|
create_atoms 1 region membrane
|
|
Created 1920 atoms
|
|
using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
|
|
create_atoms CPU = 0.001 seconds
|
|
|
|
group membrane region membrane
|
|
1920 atoms in group membrane
|
|
|
|
set type 1 mass 1.0
|
|
Setting atom values ...
|
|
1920 settings made for mass
|
|
|
|
set type 1 shape 1 0.99 0.99
|
|
Setting atom values ...
|
|
1920 settings made for shape
|
|
|
|
set group all quat 0 -1 0 90
|
|
Setting atom values ...
|
|
1920 settings made for quat
|
|
|
|
#compute memb all temp/com
|
|
#compute rot all temp/asphere bias memb
|
|
velocity all create ${T} 87287 loop geom
|
|
velocity all create 0.23 87287 loop geom
|
|
|
|
pair_style ylz 2.6
|
|
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
|
|
neighbor 1.0 bin
|
|
|
|
|
|
thermo_style custom step temp press pxx pyy
|
|
thermo 200
|
|
|
|
timestep 0.01
|
|
|
|
#dump 1 all atom 10 dump_onlymembrane.lammpstrj
|
|
|
|
fix 1 all langevin ${T} ${T} ${LD} 48279
|
|
fix 1 all langevin 0.23 ${T} ${LD} 48279
|
|
fix 1 all langevin 0.23 0.23 ${LD} 48279
|
|
fix 1 all langevin 0.23 0.23 1 48279
|
|
|
|
|
|
fix 2 all nve/asphere
|
|
run 3000
|
|
|
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
|
|
|
Your simulation uses code contributions which should be cited:
|
|
|
|
- pair ylz command:
|
|
|
|
@Article{Yuan10,
|
|
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
|
|
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
|
|
journal = {Phys. Rev. E},
|
|
year = 2010,
|
|
volume = 82,
|
|
pages = {011905}
|
|
}
|
|
|
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
|
|
|
Generated 0 of 0 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 = 3.6
|
|
ghost atom cutoff = 3.6
|
|
binsize = 1.8, bins = 22 23 65
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair ylz, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
|
|
Step Temp Press Pxx Pyy
|
|
0 0.23 -0.0073508785 -0.012283389 -0.012234574
|
|
200 0.20906916 -0.0010610794 -0.0011895359 -0.00198968
|
|
400 0.21907691 -0.00068750897 -0.0013175111 -0.00072355516
|
|
600 0.22648739 -0.00057306694 -0.000831971 -0.00096776143
|
|
800 0.2368957 -0.00028517767 -0.00050638195 -0.00052670236
|
|
1000 0.22735705 -0.00032638104 -0.00037959812 -0.00071879257
|
|
1200 0.22910882 -0.00019457758 -0.00024451315 -0.00027807764
|
|
1400 0.22754022 -0.00033048317 -0.00010053263 -0.00075173132
|
|
1600 0.22503496 -7.593954e-05 5.2989168e-05 -0.00022521685
|
|
1800 0.22673577 -0.00017917699 1.0176667e-05 -0.00047893102
|
|
2000 0.22480858 9.318318e-05 0.00031024343 1.2738253e-05
|
|
2200 0.22387294 -6.9083174e-05 -4.6170865e-05 4.6682009e-05
|
|
2400 0.22686231 0.00022776785 0.00028204391 0.00030116273
|
|
2600 0.23055637 8.2778175e-05 0.00027137529 4.2254076e-05
|
|
2800 0.23126717 0.00044863024 0.00071654709 0.00057652233
|
|
3000 0.22234736 0.00031577792 0.00051797227 0.00039087282
|
|
Loop time of 7.17991 on 1 procs for 3000 steps with 1920 atoms
|
|
|
|
Performance: 361007.348 tau/day, 417.833 timesteps/s, 802.239 katom-step/s
|
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 6.2257 | 6.2257 | 6.2257 | 0.0 | 86.71
|
|
Neigh | 0.11392 | 0.11392 | 0.11392 | 0.0 | 1.59
|
|
Comm | 0.036614 | 0.036614 | 0.036614 | 0.0 | 0.51
|
|
Output | 0.00052672 | 0.00052672 | 0.00052672 | 0.0 | 0.01
|
|
Modify | 0.78577 | 0.78577 | 0.78577 | 0.0 | 10.94
|
|
Other | | 0.01743 | | | 0.24
|
|
|
|
Nlocal: 1920 ave 1920 max 1920 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 771 ave 771 max 771 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 46750 ave 46750 max 46750 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 46750
|
|
Ave neighs/atom = 24.348958
|
|
Neighbor list builds = 98
|
|
Dangerous builds = 0
|
|
|
|
|
|
Total wall time: 0:00:07
|