diff --git a/examples/ASPHERE/flat_membrane/in_flat_membrane b/examples/ASPHERE/flat_membrane/in.flat_membrane similarity index 63% rename from examples/ASPHERE/flat_membrane/in_flat_membrane rename to examples/ASPHERE/flat_membrane/in.flat_membrane index 6efcee4640..6192485949 100644 --- a/examples/ASPHERE/flat_membrane/in_flat_membrane +++ b/examples/ASPHERE/flat_membrane/in.flat_membrane @@ -1,4 +1,4 @@ -# flat membrane demo +# flat membrane demo variable r0 equal 0.97 variable d1 equal ${r0} variable d2 equal sqrt(3.0)*${r0} @@ -6,50 +6,50 @@ variable d3 equal 3.0*${r0} variable ro equal 2./${d1}/${d2}/${d3} variable T equal 0.23 -variable LD equal 1.0 +variable LD equal 1.0 -units lj +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 + a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 -region box block 0 40 0 24 -20 20 +region box block 0 40 0 24 -20 20 create_box 1 box -region membrane block 0 40 0 24 -0.5 0.5 +region membrane block 0 40 0 24 -0.5 0.5 create_atoms 1 region membrane group membrane region membrane -set type 1 mass 1.0 +set type 1 mass 1.0 set type 1 shape 1 1 1 -set group all quat 0 -1 0 90 +set group all quat 0 -1 0 90 #compute memb all temp/com #compute rot all temp/asphere bias memb velocity all create ${T} 87287 loop geom pair_style ylz 2.6 -pair_coeff * * 1.0 1.0 4 3 0.0 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 +thermo 200 timestep 0.01 -dump 1 all atom 10 dump_onlymembrane.lammpstrj +#dump 1 all atom 10 dump_onlymembrane.lammpstrj -fix 1 all langevin ${T} ${T} ${LD} 48279 +fix 1 all langevin ${T} ${T} ${LD} 48279 -fix 2 all nve/asphere +fix 2 all nve/asphere run 3000 diff --git a/examples/ASPHERE/flat_membrane/log.lammps b/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1 similarity index 53% rename from examples/ASPHERE/flat_membrane/log.lammps rename to examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1 index c1b31e0cfe..750aa5328c 100644 --- a/examples/ASPHERE/flat_membrane/log.lammps +++ b/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1 @@ -1,6 +1,6 @@ -LAMMPS (29 Sep 2021 - Update 3) -# only membrane - +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 @@ -16,7 +16,7 @@ variable ro equal 2./0.97/1.68008928334181/2.91 variable T equal 0.23 variable LD equal 1.0 -units lj +units lj atom_style ellipsoid boundary p p p @@ -26,23 +26,23 @@ lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 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 = 0.97000000 1.6800893 2.9100000 +Lattice spacing in x,y,z = 0.97 1.6800893 2.91 -region box block 0 40 0 24 -20 20 +region box block 0 40 0 24 -20 20 create_box 1 box -Created orthogonal box = (0.0000000 0.0000000 -58.200000) to (38.800000 40.322143 58.200000) +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 = (0.0000000 0.0000000 -58.200000) to (38.800000 40.322143 58.200000) - create_atoms CPU = 0.000 seconds + 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 +set type 1 mass 1.0 Setting atom values ... 1920 settings made for mass @@ -50,12 +50,12 @@ set type 1 shape 1 1 1 Setting atom values ... 1920 settings made for shape -set group all quat 0 -1 0 90 +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 +#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 @@ -65,11 +65,11 @@ neighbor 1.0 bin thermo_style custom step temp press pxx pyy -thermo 200 +thermo 200 timestep 0.01 -dump 1 all atom 10 dump_onlymembrane.lammpstrj +#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 @@ -77,7 +77,7 @@ 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 +fix 2 all nve/asphere run 3000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE @@ -97,8 +97,9 @@ Your simulation uses code contributions which should be cited: 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 + 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 @@ -109,44 +110,44 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.097 | 6.097 | 6.097 Mbytes -Step Temp Press Pxx Pyy - 0 0.23 -0.0073508785 -0.012283389 -0.012234574 - 200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842 - 400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707 - 600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283 - 800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525 - 1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05 - 1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929 - 1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05 - 1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081 - 1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131 - 2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705 - 2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05 - 2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857 - 2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467 - 2800 0.2296401 0.00043234854 0.00058344966 0.00063645193 - 3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229 -Loop time of 5.08921 on 1 procs for 3000 steps with 1920 atoms +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 0.20903886 -0.0010605951 -0.0011885957 -0.00198842 + 400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707 + 600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283 + 800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525 + 1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05 + 1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929 + 1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05 + 1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081 + 1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131 + 2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705 + 2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05 + 2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857 + 2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467 + 2800 0.2296401 0.00043234854 0.00058344966 0.00063645193 + 3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229 +Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms -Performance: 509312.653 tau/day, 589.482 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 383058.431 tau/day, 443.355 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.2251 | 4.2251 | 4.2251 | 0.0 | 83.02 -Neigh | 0.07599 | 0.07599 | 0.07599 | 0.0 | 1.49 -Comm | 0.026195 | 0.026195 | 0.026195 | 0.0 | 0.51 -Output | 0.21176 | 0.21176 | 0.21176 | 0.0 | 4.16 -Modify | 0.53849 | 0.53849 | 0.53849 | 0.0 | 10.58 -Other | | 0.01168 | | | 0.23 +Pair | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67 +Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27 +Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51 +Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01 +Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22 +Other | | 0.02181 | | | 0.32 -Nlocal: 1920.00 ave 1920 max 1920 min +Nlocal: 1920 ave 1920 max 1920 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 772.000 ave 772 max 772 min +Nghost: 772 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 46804.0 ave 46804 max 46804 min +Neighs: 46804 ave 46804 max 46804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46804 @@ -155,7 +156,4 @@ Neighbor list builds = 99 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: 0:00:05 +Total wall time: 0:00:06 diff --git a/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 b/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 new file mode 100644 index 0000000000..7bbe99b58b --- /dev/null +++ b/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 @@ -0,0 +1,159 @@ +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 diff --git a/examples/ASPHERE/vesicle/in.vesicle b/examples/ASPHERE/vesicle/in.vesicle index 3876840d0b..ae8e2e3d75 100644 --- a/examples/ASPHERE/vesicle/in.vesicle +++ b/examples/ASPHERE/vesicle/in.vesicle @@ -1,9 +1,9 @@ -# Vesicle demo +# Vesicle demo variable T equal 0.2 -variable LD equal 1.0 +variable LD equal 1.0 -units lj +units lj atom_style ellipsoid boundary p p p @@ -16,20 +16,18 @@ compute rott all temp/asphere bias ali velocity all create ${T} 87287 loop geom pair_style ylz 2.6 -pair_coeff * * 1.0 1.0 4 3 0.0 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 +thermo 200 timestep 0.001 -dump 1 all atom 10 onlymembrane2.lammpstrj +#dump 1 all atom 10 onlymembrane2.lammpstrj -fix 1 all langevin ${T} ${T} ${LD} 48279 - - -fix 2 all nve/asphere +fix 1 all langevin ${T} ${T} ${LD} 48279 +fix 2 all nve/asphere run 3000 diff --git a/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1 b/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1 new file mode 100644 index 0000000000..f974a524e6 --- /dev/null +++ b/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1 @@ -0,0 +1,122 @@ +LAMMPS (15 Sep 2022) + using 1 OpenMP thread(s) per MPI task +# Vesicle demo + +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 -35 -35) to (35 35 35) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2938 atoms + 2938 ellipsoids + read_data CPU = 0.010 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 + +Generated 0 of 1 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 = 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) = 5.091 | 5.091 | 5.091 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 9.6866 on 1 procs for 3000 steps with 2938 atoms + +Performance: 26758.610 tau/day, 309.706 timesteps/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 | 8.3097 | 8.3097 | 8.3097 | 0.0 | 85.79 +Neigh | 0.039037 | 0.039037 | 0.039037 | 0.0 | 0.40 +Comm | 0.0021766 | 0.0021766 | 0.0021766 | 0.0 | 0.02 +Output | 0.00048628 | 0.00048628 | 0.00048628 | 0.0 | 0.01 +Modify | 1.3043 | 1.3043 | 1.3043 | 0.0 | 13.47 +Other | | 0.0309 | | | 0.32 + +Nlocal: 2938 ave 2938 max 2938 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 73242 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 + +Total wall time: 0:00:09 diff --git a/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4 b/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4 new file mode 100644 index 0000000000..0340219494 --- /dev/null +++ b/examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4 @@ -0,0 +1,122 @@ +LAMMPS (15 Sep 2022) + using 1 OpenMP thread(s) per MPI task +# Vesicle demo + +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 -35 -35) to (35 35 35) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2938 atoms + 2938 ellipsoids + read_data CPU = 0.137 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 + +Generated 0 of 1 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 = 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) = 4.899 | 4.9 | 4.902 Mbytes + Step Temp Press Pxx Pyy + 0 0.2 -0.0054891414 -0.0052713616 -0.0053641136 + 200 0.12893798 -0.0051492794 -0.0048734875 -0.0049624005 + 400 0.13798694 -0.004875313 -0.0047071897 -0.0049305051 + 600 0.14725193 -0.0046349542 -0.004719983 -0.0045791451 + 800 0.16146954 -0.0042232199 -0.0040789193 -0.0043672895 + 1000 0.17268468 -0.0037146703 -0.0036270393 -0.0039169034 + 1200 0.18266242 -0.0032749755 -0.0032971704 -0.0033323855 + 1400 0.18500165 -0.0028179031 -0.0030659821 -0.0027519633 + 1600 0.19513132 -0.0023407512 -0.0025109801 -0.0023416835 + 1800 0.19645259 -0.0019995412 -0.0019064341 -0.0021757747 + 2000 0.19658104 -0.0015897919 -0.0015850523 -0.0016828478 + 2200 0.1989936 -0.0011794062 -0.0011779716 -0.0012070706 + 2400 0.20011525 -0.0009147432 -0.00094040885 -0.001073922 + 2600 0.2013975 -0.00059253676 -0.00051920304 -0.00075138934 + 2800 0.19715513 -0.00020995605 -0.00024386426 -0.0005475745 + 3000 0.1976782 -0.0001308553 5.693004e-05 -0.00034478469 +Loop time of 8.46954 on 4 procs for 3000 steps with 2938 atoms + +Performance: 30603.800 tau/day, 354.211 timesteps/s +77.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.1751 | 2.4162 | 2.6707 | 13.2 | 28.53 +Neigh | 0.0090503 | 0.0098389 | 0.010503 | 0.6 | 0.12 +Comm | 3.5807 | 4.1526 | 4.9283 | 24.3 | 49.03 +Output | 0.00032165 | 0.0029648 | 0.010842 | 8.4 | 0.04 +Modify | 0.34554 | 0.37442 | 0.39198 | 2.8 | 4.42 +Other | | 1.514 | | | 17.87 + +Nlocal: 734.5 ave 739 max 730 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Nghost: 420.25 ave 424 max 415 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 18304.5 ave 19839 max 16636 min +Histogram: 1 0 0 0 1 0 1 0 0 1 + +Total # of neighbors = 73218 +Ave neighs/atom = 24.921035 +Neighbor list builds = 25 +Dangerous builds = 0 + +Total wall time: 0:00:08 diff --git a/examples/ASPHERE/vesicle/log.lammps b/examples/ASPHERE/vesicle/log.lammps deleted file mode 100644 index 53960d0d18..0000000000 --- a/examples/ASPHERE/vesicle/log.lammps +++ /dev/null @@ -1,124 +0,0 @@ -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