update DPD-BASIC package examples
This commit is contained in:
Axel Kohlmeyer
43
examples/PACKAGES/dpd-basic/dpd/in.dpd
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43
examples/PACKAGES/dpd-basic/dpd/in.dpd
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# DPD Fluid
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variable T equal 1.0
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variable rc equal 1.0
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variable rcD equal 1.2
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units lj
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boundary p p p
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atom_style atomic
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dimension 3
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newton on
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comm_modify vel yes
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### create box and configuration
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variable L equal 5.0
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lattice fcc 3.0
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region simBox block 0 ${L} 0 ${L} 0 ${L}
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create_box 2 simBox
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#create_atoms 1 region simBox
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create_atoms 1 random 100 12456 simBox
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create_atoms 2 random 100 13245 simBox
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mass 1 1.0
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mass 2 2.0
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###
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pair_style dpd ${T} ${rc} 3854262
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pair_coeff 1 1 25.0 4.5 1.2
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pair_coeff 1 2 25.1 4.51 1.21
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pair_coeff 2 2 25.2 4.52 1.22
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timestep 0.01
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run_style verlet
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velocity all create ${T} 68768932
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thermo_style custom step time temp press
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thermo 100
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fix 1 all nve
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run 5000
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154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.1
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154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.1
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LAMMPS (24 Mar 2022)
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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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# DPD Fluid
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variable T equal 1.0
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variable rc equal 1.0
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variable rcD equal 1.2
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units lj
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boundary p p p
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atom_style atomic
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dimension 3
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newton on
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comm_modify vel yes
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### create box and configuration
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variable L equal 5.0
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lattice fcc 3.0
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Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
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region simBox block 0 ${L} 0 ${L} 0 ${L}
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region simBox block 0 5 0 ${L} 0 ${L}
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region simBox block 0 5 0 5 0 ${L}
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region simBox block 0 5 0 5 0 5
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create_box 2 simBox
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Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
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1 by 1 by 1 MPI processor grid
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#create_atoms 1 region simBox
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create_atoms 1 random 100 12456 simBox
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Created 100 atoms
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using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
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create_atoms CPU = 0.000 seconds
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create_atoms 2 random 100 13245 simBox
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Created 100 atoms
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using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
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create_atoms CPU = 0.000 seconds
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mass 1 1.0
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mass 2 2.0
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###
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pair_style dpd ${T} ${rc} 3854262
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pair_style dpd 1 ${rc} 3854262
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pair_style dpd 1 1 3854262
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pair_coeff 1 1 25.0 4.5 1.2
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pair_coeff 1 2 25.1 4.51 1.21
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pair_coeff 2 2 25.2 4.52 1.22
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timestep 0.01
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run_style verlet
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velocity all create ${T} 68768932
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velocity all create 1 68768932
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thermo_style custom step time temp press
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thermo 100
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fix 1 all nve
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run 5000
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generated 0 of 1 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 = 1.52
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ghost atom cutoff = 1.52
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binsize = 0.76, bins = 8 8 8
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair dpd, 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) = 3.083 | 3.083 | 3.083 Mbytes
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Step Time Temp Press
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0 0 1 9.5226009
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100 1 1.9913643 9.2036029
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200 2 1.6321732 9.2787957
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300 3 1.3533438 8.3081433
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400 4 1.2125884 8.0809065
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500 5 1.0682216 8.0877925
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600 6 0.99100473 8.1100319
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700 7 0.99731243 7.8225195
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800 8 1.0597693 7.8368218
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900 9 0.99038588 7.9450569
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1000 10 1.077129 7.5857015
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1100 11 0.99070336 7.5138128
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1200 12 1.013894 7.2794857
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1300 13 1.0433203 7.7439871
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1400 14 1.0285528 7.5662235
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1500 15 0.99180601 7.8376313
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1600 16 0.98059071 8.0243735
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1700 17 1.0070947 8.3186893
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1800 18 0.99507569 7.0786393
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1900 19 1.0040168 7.8120389
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2000 20 0.98636164 7.472185
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2100 21 0.95811165 7.7085985
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2200 22 0.93568327 6.9424246
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2300 23 0.92804144 8.1239435
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2400 24 0.94940276 7.6108611
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2500 25 1.0535153 8.0772721
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2600 26 1.0902144 7.5609768
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2700 27 1.0737336 7.8706755
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2800 28 0.93074581 7.3699993
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2900 29 1.0440705 7.6454988
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3000 30 0.93868164 7.841168
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3100 31 1.0172025 7.6856163
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3200 32 1.0405368 7.5325735
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3300 33 0.96721201 7.8262809
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3400 34 0.90430758 7.1693921
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3500 35 0.89938433 7.865845
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3600 36 0.9907178 7.3462971
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3700 37 1.0311879 7.8876401
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3800 38 0.98339132 7.3413929
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3900 39 1.2111264 8.0968408
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4000 40 1.062489 7.7315959
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4100 41 0.94737492 7.3386028
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4200 42 1.0453816 8.2017304
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4300 43 0.97024897 7.7379624
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4400 44 0.9553861 7.8047635
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4500 45 1.043252 7.7486215
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4600 46 0.98611474 8.1237053
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4700 47 0.98624285 8.5801642
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4800 48 0.97176754 7.1540299
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4900 49 1.0165401 7.3853841
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5000 50 0.88359115 7.5541592
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Loop time of 0.359916 on 1 procs for 5000 steps with 200 atoms
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Performance: 12002788.048 tau/day, 13892.116 timesteps/s
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99.5% 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 | 0.24932 | 0.24932 | 0.24932 | 0.0 | 69.27
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Neigh | 0.068726 | 0.068726 | 0.068726 | 0.0 | 19.10
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Comm | 0.028691 | 0.028691 | 0.028691 | 0.0 | 7.97
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Output | 0.00066318 | 0.00066318 | 0.00066318 | 0.0 | 0.18
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Modify | 0.0078062 | 0.0078062 | 0.0078062 | 0.0 | 2.17
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Other | | 0.004713 | | | 1.31
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Nlocal: 200 ave 200 max 200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 546 ave 546 max 546 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1649 ave 1649 max 1649 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1649
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Ave neighs/atom = 8.245
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Neighbor list builds = 500
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Dangerous builds = 500
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Total wall time: 0:00:00
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154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.4
Normal file
154
examples/PACKAGES/dpd-basic/dpd/log.5Apr22.dpd.g++.4
Normal file
@ -0,0 +1,154 @@
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LAMMPS (24 Mar 2022)
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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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# DPD Fluid
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variable T equal 1.0
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variable rc equal 1.0
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variable rcD equal 1.2
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units lj
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boundary p p p
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atom_style atomic
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dimension 3
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newton on
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comm_modify vel yes
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### create box and configuration
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variable L equal 5.0
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lattice fcc 3.0
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Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
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region simBox block 0 ${L} 0 ${L} 0 ${L}
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region simBox block 0 5 0 ${L} 0 ${L}
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region simBox block 0 5 0 5 0 ${L}
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region simBox block 0 5 0 5 0 5
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create_box 2 simBox
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Created orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
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1 by 2 by 2 MPI processor grid
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#create_atoms 1 region simBox
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create_atoms 1 random 100 12456 simBox
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Created 100 atoms
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using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
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create_atoms CPU = 0.000 seconds
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create_atoms 2 random 100 13245 simBox
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Created 100 atoms
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using lattice units in orthogonal box = (0 0 0) to (5.5032121 5.5032121 5.5032121)
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create_atoms CPU = 0.000 seconds
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mass 1 1.0
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mass 2 2.0
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###
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pair_style dpd ${T} ${rc} 3854262
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pair_style dpd 1 ${rc} 3854262
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pair_style dpd 1 1 3854262
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pair_coeff 1 1 25.0 4.5 1.2
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pair_coeff 1 2 25.1 4.51 1.21
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pair_coeff 2 2 25.2 4.52 1.22
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timestep 0.01
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run_style verlet
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velocity all create ${T} 68768932
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velocity all create 1 68768932
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thermo_style custom step time temp press
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thermo 100
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fix 1 all nve
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run 5000
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generated 0 of 1 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 = 1.52
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ghost atom cutoff = 1.52
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binsize = 0.76, bins = 8 8 8
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair dpd, 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) = 3.064 | 3.064 | 3.064 Mbytes
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Step Time Temp Press
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0 0 1 8.603339
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100 1 1.8691059 8.9058297
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200 2 1.4500635 8.7420141
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300 3 1.3089453 8.3985981
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400 4 1.1647803 8.2948808
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500 5 1.1399445 7.7421817
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600 6 1.0297918 7.2040397
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700 7 1.046713 7.6115758
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800 8 0.93523712 7.6885563
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900 9 0.94701493 7.9662712
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1000 10 0.99302416 7.7606189
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1100 11 0.98975674 7.5207427
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1200 12 0.98661662 7.3565222
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1300 13 1.0289377 7.6110453
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1400 14 0.9982501 7.8065701
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1500 15 1.0043888 7.3957185
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1600 16 1.0175816 7.7885955
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1700 17 1.0252117 7.5076258
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1800 18 1.0275139 8.1052823
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1900 19 1.0021054 7.0385989
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2000 20 1.0489009 7.7138149
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2100 21 0.91250488 7.3540839
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2200 22 0.92470996 7.9600233
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2300 23 0.96932725 7.3106045
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2400 24 0.93443088 7.4594635
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2500 25 0.95596038 7.2544715
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2600 26 1.0368594 7.6229263
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2700 27 0.94639332 7.4869636
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2800 28 0.99917354 7.9806636
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2900 29 0.95048071 7.0086404
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3000 30 0.95226181 7.7807205
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3100 31 0.95864429 7.8059442
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3200 32 0.85678761 7.3416027
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3300 33 0.95951096 7.3467158
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3400 34 0.97665772 8.2900991
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3500 35 0.92885927 7.5385993
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3600 36 1.0455015 8.0627999
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3700 37 0.91911809 8.0371736
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3800 38 0.92022241 7.5803999
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3900 39 1.0465522 7.6920189
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4000 40 0.98568475 7.4529825
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4100 41 1.0389372 7.2273346
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4200 42 1.0257545 7.6081878
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4300 43 1.0937573 8.2158237
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4400 44 1.0908817 7.5021567
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4500 45 1.0482874 7.5924368
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4600 46 1.1468439 8.0285157
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4700 47 1.119683 8.3365123
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4800 48 1.0963877 7.51772
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4900 49 1.0766762 7.3137035
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5000 50 1.0359203 7.7354572
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Loop time of 0.148597 on 4 procs for 5000 steps with 200 atoms
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Performance: 29071936.422 tau/day, 33648.075 timesteps/s
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98.8% 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 | 0.059602 | 0.063397 | 0.068622 | 1.3 | 42.66
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Neigh | 0.017747 | 0.018193 | 0.018698 | 0.3 | 12.24
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Comm | 0.055145 | 0.061014 | 0.065369 | 1.5 | 41.06
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Output | 0.00042708 | 0.00050725 | 0.00071024 | 0.0 | 0.34
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Modify | 0.0023494 | 0.002532 | 0.0026434 | 0.2 | 1.70
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Other | | 0.002953 | | | 1.99
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Nlocal: 50 ave 52 max 48 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Nghost: 292.75 ave 299 max 287 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 413.5 ave 441 max 399 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Total # of neighbors = 1654
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Ave neighs/atom = 8.27
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Neighbor list builds = 500
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Dangerous builds = 500
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Total wall time: 0:00:00
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