update examples to match others
This commit is contained in:
Axel Kohlmeyer
@ -44,7 +44,7 @@ thermo 200
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timestep 0.01
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timestep 0.01
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dump 1 all atom 10 dump_onlymembrane.lammpstrj
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#dump 1 all atom 10 dump_onlymembrane.lammpstrj
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fix 1 all langevin ${T} ${T} ${LD} 48279
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fix 1 all langevin ${T} ${T} ${LD} 48279
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@ -1,6 +1,6 @@
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LAMMPS (29 Sep 2021 - Update 3)
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LAMMPS (15 Sep 2022)
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# only membrane
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using 1 OpenMP thread(s) per MPI task
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# flat membrane demo
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variable r0 equal 0.97
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variable r0 equal 0.97
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variable d1 equal ${r0}
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variable d1 equal ${r0}
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variable d1 equal 0.97
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variable d1 equal 0.97
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@ -26,18 +26,18 @@ lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0
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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
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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
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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
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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
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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
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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
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Lattice spacing in x,y,z = 0.97000000 1.6800893 2.9100000
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Lattice spacing in x,y,z = 0.97 1.6800893 2.91
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region box block 0 40 0 24 -20 20
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region box block 0 40 0 24 -20 20
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create_box 1 box
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create_box 1 box
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Created orthogonal box = (0.0000000 0.0000000 -58.200000) to (38.800000 40.322143 58.200000)
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Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
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1 by 1 by 1 MPI processor grid
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1 by 1 by 1 MPI processor grid
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region membrane block 0 40 0 24 -0.5 0.5
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region membrane block 0 40 0 24 -0.5 0.5
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create_atoms 1 region membrane
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create_atoms 1 region membrane
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Created 1920 atoms
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Created 1920 atoms
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using lattice units in orthogonal box = (0.0000000 0.0000000 -58.200000) to (38.800000 40.322143 58.200000)
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using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
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create_atoms CPU = 0.000 seconds
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create_atoms CPU = 0.001 seconds
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group membrane region membrane
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group membrane region membrane
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1920 atoms in group membrane
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1920 atoms in group membrane
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@ -54,8 +54,8 @@ set group all quat 0 -1 0 90
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Setting atom values ...
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Setting atom values ...
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1920 settings made for quat
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1920 settings made for quat
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compute memb all temp/com
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#compute memb all temp/com
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compute rot all temp/asphere bias memb
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#compute rot all temp/asphere bias memb
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velocity all create ${T} 87287 loop geom
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velocity all create ${T} 87287 loop geom
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velocity all create 0.23 87287 loop geom
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velocity all create 0.23 87287 loop geom
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@ -69,7 +69,7 @@ thermo 200
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timestep 0.01
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timestep 0.01
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dump 1 all atom 10 dump_onlymembrane.lammpstrj
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#dump 1 all atom 10 dump_onlymembrane.lammpstrj
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fix 1 all langevin ${T} ${T} ${LD} 48279
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fix 1 all langevin ${T} ${T} ${LD} 48279
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fix 1 all langevin 0.23 ${T} ${LD} 48279
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fix 1 all langevin 0.23 ${T} ${LD} 48279
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@ -97,8 +97,9 @@ Your simulation uses code contributions which should be cited:
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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update: every = 1 steps, delay = 10 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.6
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master list distance cutoff = 3.6
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ghost atom cutoff = 3.6
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ghost atom cutoff = 3.6
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@ -109,8 +110,8 @@ Neighbor list info ...
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pair build: half/bin/atomonly/newton
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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stencil: half/bin/3d
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bin: standard
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.097 | 6.097 | 6.097 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
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Step Temp Press Pxx Pyy
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Step Temp Press Pxx Pyy
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0 0.23 -0.0073508785 -0.012283389 -0.012234574
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0 0.23 -0.0073508785 -0.012283389 -0.012234574
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200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
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200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
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400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
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400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
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@ -127,26 +128,26 @@ Step Temp Press Pxx Pyy
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2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
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2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
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2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
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2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
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3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
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3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
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Loop time of 5.08921 on 1 procs for 3000 steps with 1920 atoms
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Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms
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Performance: 509312.653 tau/day, 589.482 timesteps/s
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Performance: 383058.431 tau/day, 443.355 timesteps/s
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99.7% CPU use with 1 MPI tasks x no OpenMP threads
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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---------------------------------------------------------------
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Pair | 4.2251 | 4.2251 | 4.2251 | 0.0 | 83.02
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Pair | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67
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Neigh | 0.07599 | 0.07599 | 0.07599 | 0.0 | 1.49
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Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27
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Comm | 0.026195 | 0.026195 | 0.026195 | 0.0 | 0.51
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Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51
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Output | 0.21176 | 0.21176 | 0.21176 | 0.0 | 4.16
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Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01
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Modify | 0.53849 | 0.53849 | 0.53849 | 0.0 | 10.58
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Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22
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Other | | 0.01168 | | | 0.23
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Other | | 0.02181 | | | 0.32
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Nlocal: 1920.00 ave 1920 max 1920 min
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Nlocal: 1920 ave 1920 max 1920 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 772.000 ave 772 max 772 min
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Nghost: 772 ave 772 max 772 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 46804.0 ave 46804 max 46804 min
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Neighs: 46804 ave 46804 max 46804 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 46804
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Total # of neighbors = 46804
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@ -155,7 +156,4 @@ Neighbor list builds = 99
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Dangerous builds = 0
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Dangerous builds = 0
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# 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.
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Total wall time: 0:00:06
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# notes-2: drag=0.2 is effective for control pressure, pressure reach desired value too slow if no drag
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# notes-3: pressure reach equilibrium much quicker than temperature
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Total wall time: 0:00:05
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159
examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4
Normal file
159
examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4
Normal file
@ -0,0 +1,159 @@
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LAMMPS (15 Sep 2022)
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using 1 OpenMP thread(s) per MPI task
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# flat membrane demo
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variable r0 equal 0.97
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variable d1 equal ${r0}
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variable d1 equal 0.97
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variable d2 equal sqrt(3.0)*${r0}
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variable d2 equal sqrt(3.0)*0.97
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variable d3 equal 3.0*${r0}
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variable d3 equal 3.0*0.97
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variable ro equal 2./${d1}/${d2}/${d3}
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variable ro equal 2./0.97/${d2}/${d3}
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variable ro equal 2./0.97/1.68008928334181/${d3}
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variable ro equal 2./0.97/1.68008928334181/2.91
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variable T equal 0.23
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variable LD equal 1.0
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units lj
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atom_style ellipsoid
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boundary p p p
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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
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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
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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
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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
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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
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Lattice spacing in x,y,z = 0.97 1.6800893 2.91
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region box block 0 40 0 24 -20 20
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create_box 1 box
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Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
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1 by 1 by 4 MPI processor grid
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region membrane block 0 40 0 24 -0.5 0.5
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create_atoms 1 region membrane
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Created 1920 atoms
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using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
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create_atoms CPU = 0.001 seconds
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group membrane region membrane
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1920 atoms in group membrane
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set type 1 mass 1.0
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Setting atom values ...
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1920 settings made for mass
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set type 1 shape 1 1 1
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Setting atom values ...
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1920 settings made for shape
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set group all quat 0 -1 0 90
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Setting atom values ...
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1920 settings made for quat
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#compute memb all temp/com
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#compute rot all temp/asphere bias memb
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velocity all create ${T} 87287 loop geom
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velocity all create 0.23 87287 loop geom
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pair_style ylz 2.6
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pair_coeff * * 1.0 1.0 4 3 0.0 2.6
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neighbor 1.0 bin
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thermo_style custom step temp press pxx pyy
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thermo 200
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timestep 0.01
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#dump 1 all atom 10 dump_onlymembrane.lammpstrj
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fix 1 all langevin ${T} ${T} ${LD} 48279
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fix 1 all langevin 0.23 ${T} ${LD} 48279
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fix 1 all langevin 0.23 0.23 ${LD} 48279
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fix 1 all langevin 0.23 0.23 1 48279
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fix 2 all nve/asphere
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run 3000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- pair ylz command:
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@Article{Yuan10,
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author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
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title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
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journal = {Phys. Rev. E},
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year = 2010,
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volume = 82,
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pages = {011905}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 10 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.6
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ghost atom cutoff = 3.6
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binsize = 1.8, bins = 22 23 65
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair ylz, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes
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Step Temp Press Pxx Pyy
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0 0.23 -0.0073508785 -0.012283389 -0.012234574
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200 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502
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400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093
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600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609
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800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294
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1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572
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1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505
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1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05
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1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754
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1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05
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2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213
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2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05
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2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05
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2600 0.23085675 0.00014029405 0.00017983536 0.00017895001
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2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243
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3000 0.23421357 0.00023505702 0.00020752013 0.00053567111
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Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms
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Performance: 553164.568 tau/day, 640.237 timesteps/s
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95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21
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Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54
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Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28
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Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50
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Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57
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Other | | 2.338 | | | 49.90
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Nlocal: 480 ave 1011 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Nghost: 860 ave 1771 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 11697.8 ave 30095 max 0 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Total # of neighbors = 46791
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Ave neighs/atom = 24.370313
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Neighbor list builds = 99
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Dangerous builds = 0
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Total wall time: 0:00:04
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@ -24,11 +24,9 @@ thermo 200
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|
||||||
timestep 0.001
|
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 1 all langevin ${T} ${T} ${LD} 48279
|
||||||
|
|
||||||
|
|
||||||
fix 2 all nve/asphere
|
fix 2 all nve/asphere
|
||||||
|
|
||||||
run 3000
|
run 3000
|
||||||
|
|||||||
122
examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1
Normal file
122
examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1
Normal file
@ -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
|
||||||
122
examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4
Normal file
122
examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4
Normal file
@ -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
|
||||||
@ -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
|
|
||||||
Reference in New Issue
Block a user