LAMMPS (15 Sep 2022) 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 4 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 1 1 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 = 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 = 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) = 4.182 | 4.794 | 5.472 Mbytes Step Temp Press Pxx Pyy 0 0.23 -0.0073508785 -0.012283389 -0.012234574 200 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502 400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093 600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609 800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294 1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572 1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505 1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05 1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754 1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05 2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213 2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05 2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05 2600 0.23085675 0.00014029405 0.00017983536 0.00017895001 2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243 3000 0.23421357 0.00023505702 0.00020752013 0.00053567111 Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms Performance: 553164.568 tau/day, 640.237 timesteps/s 95.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21 Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54 Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28 Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50 Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57 Other | | 2.338 | | | 49.90 Nlocal: 480 ave 1011 max 0 min Histogram: 2 0 0 0 0 0 0 0 1 1 Nghost: 860 ave 1771 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 11697.8 ave 30095 max 0 min Histogram: 2 0 0 0 0 1 0 0 0 1 Total # of neighbors = 46791 Ave neighs/atom = 24.370313 Neighbor list builds = 99 Dangerous builds = 0 Total wall time: 0:00:04