LAMMPS (29 Sep 2021 - Update 3) variable T equal 0.2 variable LD equal 1.0 units lj atom_style ellipsoid boundary p p p read_data read_data.vesicle1026 Reading data file ... orthogonal box = (-35.000000 -35.000000 -35.000000) to (35.000000 35.000000 35.000000) 1 by 1 by 1 MPI processor grid reading atoms ... 2938 atoms 2938 ellipsoids read_data CPU = 0.008 seconds compute ali all temp/com compute rott all temp/asphere bias ali velocity all create ${T} 87287 loop geom velocity all create 0.2 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 0.001 dump 1 all atom 10 onlymembrane2.lammpstrj fix 1 all langevin ${T} ${T} ${LD} 48279 fix 1 all langevin 0.2 ${T} ${LD} 48279 fix 1 all langevin 0.2 0.2 ${LD} 48279 fix 1 all langevin 0.2 0.2 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 Neighbor list info ... update every 1 steps, delay 10 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 = 39 39 39 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) = 6.203 | 6.203 | 6.203 Mbytes Step Temp Press Pxx Pyy 0 0.2 -0.0054891414 -0.0052713616 -0.0053641136 200 0.12816247 -0.0051288861 -0.0048542514 -0.0049847561 400 0.1377632 -0.0048071582 -0.0045651263 -0.0048444087 600 0.14983781 -0.0045305725 -0.0043305994 -0.0046127777 800 0.16205271 -0.0041176346 -0.0040534483 -0.0041351779 1000 0.17462122 -0.0037000069 -0.0034938539 -0.0037915494 1200 0.18335448 -0.0032674318 -0.0032790248 -0.0031967931 1400 0.19195613 -0.0029332101 -0.0030823703 -0.0028287799 1600 0.19261762 -0.0025263447 -0.0025152249 -0.0026205398 1800 0.19758674 -0.0021087725 -0.001981333 -0.002309048 2000 0.19748896 -0.0017662369 -0.0019316344 -0.0016696035 2200 0.20196986 -0.0013363214 -0.0015581191 -0.0013384961 2400 0.20109248 -0.0009190831 -0.0010331417 -0.0010664316 2600 0.20228664 -0.00053590675 -0.00071808747 -0.00050218533 2800 0.20512955 -0.00030845899 -0.00016244901 -0.00047877516 3000 0.19855941 -7.9520073e-05 -0.00014969215 -5.4724226e-06 Loop time of 7.2222 on 1 procs for 3000 steps with 2938 atoms Performance: 35889.329 tau/day, 415.386 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0158 | 6.0158 | 6.0158 | 0.0 | 83.30 Neigh | 0.034308 | 0.034308 | 0.034308 | 0.0 | 0.48 Comm | 0.0015149 | 0.0015149 | 0.0015149 | 0.0 | 0.02 Output | 0.31567 | 0.31567 | 0.31567 | 0.0 | 4.37 Modify | 0.83787 | 0.83787 | 0.83787 | 0.0 | 11.60 Other | | 0.01702 | | | 0.24 Nlocal: 2938.00 ave 2938 max 2938 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: 73242.0 ave 73242 max 73242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73242 Ave neighs/atom = 24.929204 Neighbor list builds = 26 Dangerous builds = 0 # notes-1: for npt control, t_start,p_start don't need to be the same as real staring value, moreover, it can cause problem. # notes-2: drag=0.2 is effective for control pressure, pressure reach desired value too slow if no drag # notes-3: pressure reach equilibrium much quicker than temperature Total wall time: 0:00:07