176 lines
7.6 KiB
Groff
176 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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### Heat conduction analog of periodic Poiseuille flow problem ###
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### using energy-conserving DPD (eDPD) 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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### mDPD system setup follows Fig.12 in the publication: ###
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### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
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### "Energy-conserving dissipative particle dynamics with ###
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### temperature-dependent properties". J. Comput. Phys., ###
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### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
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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 edpd
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comm_modify vel yes
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region edpd block -10 10 -10 10 -5 5 units box
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create_box 1 edpd
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Created orthogonal box = (-10 -10 -5) to (10 10 5)
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1 by 1 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 * edpd/temp 1.0
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Setting atom values ...
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16000 settings made for edpd/temp
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set atom * edpd/cv 1.0E5
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Setting atom values ...
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16000 settings made for edpd/cv
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pair_style edpd 1.58 9872598
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#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
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pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
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compute mythermo all temp
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thermo 100
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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/edpd 0.5
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fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
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fix lower all edpd/source 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 edpd command: doi:10.1016/j.jcp.2014.02.003
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@Article{ZLi2014_JCP,
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author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G. E.},
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title = {Energy-Conserving Dissipative Particle Dynamics with Temperature-Dependent Properties},
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journal = {Journal of Computational Physics},
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year = {2014},
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volume = {265},
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pages = {113--127}
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}
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@Article{ZLi2015_CC,
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author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G. E.},
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title = {Mesoscale Modeling of Phase Transition Dynamics of Thermoresponsive Polymers},
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journal = {Chemical Communications},
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year = {2015},
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volume = {51},
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pages = {11038--11040}
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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 edpd, 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) = 12.1 | 12.1 | 12.1 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 48.942039 0 50.441946 201.43068
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100 0.99644296 43.749732 0 45.244303 200.44316
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200 0.98985852 43.699081 0 45.183776 197.29314
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300 1.0062075 43.708406 0 45.217622 194.61595
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400 0.99858259 43.69758 0 45.19536 196.87253
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500 0.99991379 43.677571 0 45.177348 194.59785
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Loop time of 48.2916 on 1 procs for 500 steps with 16000 atoms
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Performance: 8945.662 tau/day, 10.354 timesteps/s, 165.660 katom-step/s
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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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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 43.121 | 43.121 | 43.121 | 0.0 | 89.29
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Neigh | 4.5712 | 4.5712 | 4.5712 | 0.0 | 9.47
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Comm | 0.28793 | 0.28793 | 0.28793 | 0.0 | 0.60
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Output | 0.00040031 | 0.00040031 | 0.00040031 | 0.0 | 0.00
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Modify | 0.24651 | 0.24651 | 0.24651 | 0.0 | 0.51
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Other | | 0.06435 | | | 0.13
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Nlocal: 16000 ave 16000 max 16000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 14106 ave 14106 max 14106 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 749963 ave 749963 max 749963 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 749963
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Ave neighs/atom = 46.872687
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Neighbor list builds = 181
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Dangerous builds = 0
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reset_timestep 0
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compute temp all edpd/temp/atom
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compute ccT all chunk/atom bin/1d y 0.0 1.0
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fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
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run 500
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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) = 12.6 | 12.6 | 12.6 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.99991379 43.67752 0 45.177297 195.4932
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100 1.0053402 43.685038 0 45.192954 196.73683
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200 1.0052797 43.665955 0 45.173781 198.60396
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300 0.98694632 43.650877 0 45.131204 199.11464
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400 1.003189 43.639966 0 45.144655 196.20663
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500 1.008172 43.625425 0 45.137589 196.69792
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Loop time of 47.2499 on 1 procs for 500 steps with 16000 atoms
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Performance: 9142.877 tau/day, 10.582 timesteps/s, 169.313 katom-step/s
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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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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 42.09 | 42.09 | 42.09 | 0.0 | 89.08
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Neigh | 4.4695 | 4.4695 | 4.4695 | 0.0 | 9.46
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Comm | 0.28364 | 0.28364 | 0.28364 | 0.0 | 0.60
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Output | 0.00041768 | 0.00041768 | 0.00041768 | 0.0 | 0.00
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Modify | 0.34551 | 0.34551 | 0.34551 | 0.0 | 0.73
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Other | | 0.06079 | | | 0.13
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Nlocal: 16000 ave 16000 max 16000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 14131 ave 14131 max 14131 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 749932 ave 749932 max 749932 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 749932
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Ave neighs/atom = 46.87075
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Neighbor list builds = 182
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Dangerous builds = 0
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Total wall time: 0:01:35
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