172 lines
7.6 KiB
Groff
172 lines
7.6 KiB
Groff
LAMMPS (28 Mar 2023 - Development)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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########################################################################
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### Pure diffusion with a reaction source term analog of a periodic ###
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### Poiseuille flow problem using transport DPD (tDPD) simulation ###
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### ###
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### Created : Zhen Li (zhen_li@brown.edu) ###
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### Division of Applied Mathematics, Brown University. ###
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### ###
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### tDPD system setup follows Fig.1 in the publication: ###
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### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
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### "Transport dissipative particle dynamics model for mesoscopic ###
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### advection-diffusion-reaction problems. J. Chem. Phys., ###
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### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
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########################################################################
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units lj
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dimension 3
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boundary p p p
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neighbor 0.2 bin
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neigh_modify every 1 delay 0 check yes
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atom_style tdpd 2
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comm_modify vel yes
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region tdpd block -10 10 -10 10 -5 5 units box
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create_box 1 tdpd
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Created orthogonal box = (-10 -10 -5) to (10 10 5)
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2 by 2 by 1 MPI processor grid
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create_atoms 1 random 16000 276438 NULL
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Created 16000 atoms
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using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
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create_atoms CPU = 0.002 seconds
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mass 1 1.0
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set atom * cc 1 1.0
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Setting atom values ...
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16000 settings made for cc index 1
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set atom * cc 2 1.0
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Setting atom values ...
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16000 settings made for cc index 2
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pair_style tdpd 1.0 1.58 9872598
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pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
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compute mythermo all temp
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thermo 50
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thermo_modify temp mythermo
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thermo_modify flush yes
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velocity all create 1.0 432982 loop local dist gaussian
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fix mvv all mvv/tdpd 0.5
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fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
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fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
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fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
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fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
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timestep 0.01
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run 500
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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 tdpd command: doi:10.1063/1.4923254
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@Article{ZLi2015_JCP,
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author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G. E.},
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title = {Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-Diffusion-Reaction Problems},
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journal = {The Journal of Chemical Physics},
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year = {2015},
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volume = {143},
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number = {1},
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pages = {014101}
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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 = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.78
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ghost atom cutoff = 1.78
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binsize = 0.89, bins = 23 23 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tdpd, 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) = 5.337 | 5.351 | 5.36 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 48.942039 0 50.441946 199.59508
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50 1.0164166 43.95706 0 45.48159 198.02944
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100 0.99583217 43.760777 0 45.254431 198.26943
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150 1.0025022 43.730114 0 45.233774 198.402
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200 0.99563635 43.72379 0 45.217151 197.6948
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250 1.0117752 43.724349 0 45.241917 195.70427
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300 0.98950567 43.72333 0 45.207496 197.582
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350 0.99351667 43.719413 0 45.209595 194.69504
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400 1.0050663 43.715857 0 45.223362 198.50199
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450 1.003148 43.712337 0 45.216965 196.26462
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500 0.99888463 43.712357 0 45.21059 195.78645
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Loop time of 16.464 on 4 procs for 500 steps with 16000 atoms
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Performance: 26239.140 tau/day, 30.369 timesteps/s, 485.910 katom-step/s
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99.6% 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 | 14.166 | 14.302 | 14.373 | 2.1 | 86.87
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Neigh | 1.406 | 1.4132 | 1.4179 | 0.4 | 8.58
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Comm | 0.53805 | 0.61257 | 0.75493 | 10.7 | 3.72
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Output | 0.00041375 | 0.00062178 | 0.00091415 | 0.0 | 0.00
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Modify | 0.088249 | 0.089209 | 0.090198 | 0.2 | 0.54
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Other | | 0.04683 | | | 0.28
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Nlocal: 4000 ave 4013 max 3992 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Nghost: 5990 ave 6012 max 5980 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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Neighs: 187350 ave 188412 max 186633 min
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Histogram: 1 0 1 1 0 0 0 0 0 1
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Total # of neighbors = 749401
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Ave neighs/atom = 46.837562
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Neighbor list builds = 182
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Dangerous builds = 0
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reset_timestep 0
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compute cc1 all tdpd/cc/atom 1
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compute cc2 all tdpd/cc/atom 2
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compute bin all chunk/atom bin/1d y 0.0 1.0
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fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
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run 100
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 5.588 | 5.602 | 5.61 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.99888463 43.712357 0 45.21059 197.42728
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50 1.0015386 43.71567 0 45.217884 198.28372
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100 1.0053363 43.718221 0 45.226131 195.45072
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Loop time of 3.09095 on 4 procs for 100 steps with 16000 atoms
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Performance: 27952.588 tau/day, 32.353 timesteps/s, 517.641 katom-step/s
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99.7% 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 | 2.6867 | 2.6999 | 2.7131 | 0.8 | 87.35
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Neigh | 0.2523 | 0.25332 | 0.25501 | 0.2 | 8.20
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Comm | 0.087738 | 0.10048 | 0.11401 | 4.0 | 3.25
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Output | 0.00014184 | 0.00015461 | 0.00015946 | 0.0 | 0.01
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Modify | 0.028066 | 0.028154 | 0.02831 | 0.1 | 0.91
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Other | | 0.008906 | | | 0.29
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Nlocal: 4000 ave 4024 max 3988 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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Nghost: 5977 ave 6004 max 5941 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Neighs: 187313 ave 188798 max 186723 min
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Histogram: 2 1 0 0 0 0 0 0 0 1
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Total # of neighbors = 749253
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Ave neighs/atom = 46.828313
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Neighbor list builds = 35
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Dangerous builds = 0
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Total wall time: 0:00:19
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