222 lines
9.9 KiB
Groff
222 lines
9.9 KiB
Groff
LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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# 2D overdamped active brownian particle dynamics (ABP)
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# with WCA potential
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variable gamma_t string 1.0
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variable gamma_r string 1.0
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variable temp string 1.0
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variable seed equal 1974019
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variable fp string 4.0
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variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
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variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
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variable params string 1.0_1.0_${gamma_r}_${fp}
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variable params string 1.0_1.0_1.0_${fp}
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variable params string 1.0_1.0_1.0_4.0
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units lj
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atom_style hybrid dipole sphere
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WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
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dimension 2
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newton off
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lattice sq 0.4
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Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
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region box block -16 16 -16 16 -0.2 0.2
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create_box 1 box
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Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 1024 atoms
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create_atoms CPU = 0.002 seconds
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mass * 1.0
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set type * dipole/random ${seed} 1.0
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set type * dipole/random 1974019 1.0
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Setting atom values ...
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1024 settings made for dipole/random
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velocity all create 1.0 1 loop geom
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# more careful with neighbors since higher diffusion in abps
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neighbor 1.0 bin
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neigh_modify every 1 delay 1 check yes
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# WCA potential (purely repulsive)
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 1.1224
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pair_modify shift yes
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# overdamped brownian dynamics time-step
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fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
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fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
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fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
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fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r ${gamma_r}
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fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r 1.0
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# self-propulsion force along the dipole direction
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fix activity all propel/self dipole ${fp}
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fix activity all propel/self dipole 4.0
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fix 2 all enforce2d
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compute press all pressure NULL virial
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thermo_style custom step pe ke c_press
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#equilibration
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timestep 0.0000000001
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thermo 100
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run 5000
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Neighbor list info ...
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update every 1 steps, delay 1 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.1224
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ghost atom cutoff = 2.1224
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binsize = 1.0612, bins = 48 48 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: half/bin/2d/newtoff
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes
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Step PotEng KinEng c_press
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0 0 0.99902344 -0.53979198
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100 0 1.026585e+10 -0.5398101
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200 0 1.0630628e+10 -0.53977393
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300 0 1.03483e+10 -0.53977041
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400 0 1.049279e+10 -0.53974314
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500 0 1.0832067e+10 -0.53979451
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600 0 1.0403632e+10 -0.53976233
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700 0 1.0334726e+10 -0.53976174
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800 0 1.0119596e+10 -0.53969338
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900 0 1.0786136e+10 -0.53970415
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1000 0 1.0539036e+10 -0.53974577
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1100 0 1.0643695e+10 -0.53982431
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1200 0 1.0234642e+10 -0.53976823
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1300 0 1.036268e+10 -0.53981454
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1400 0 1.0605702e+10 -0.53988117
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1500 0 1.0517916e+10 -0.53989207
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1600 0 1.0564482e+10 -0.53993016
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1700 0 1.0460152e+10 -0.53984454
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1800 0 1.0468566e+10 -0.53985574
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1900 0 1.0474075e+10 -0.53985439
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2000 0 1.0683568e+10 -0.53987349
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2100 0 1.0269077e+10 -0.53990709
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2200 0 1.0386943e+10 -0.53990068
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2300 0 1.0406078e+10 -0.53978402
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2400 0 1.0482072e+10 -0.53980757
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2500 0 1.0442975e+10 -0.53982657
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2600 0 1.0292103e+10 -0.53985533
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2700 0 1.1106453e+10 -0.53991861
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2800 0 1.0395289e+10 -0.53990138
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2900 0 1.034021e+10 -0.53992375
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3000 0 1.0434718e+10 -0.53995566
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3100 0 1.0194094e+10 -0.53993997
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3200 0 1.0411552e+10 -0.54000097
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3300 0 1.0214175e+10 -0.53999884
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3400 0 1.0434719e+10 -0.54000005
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3500 0 1.0529638e+10 -0.53998281
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3600 0 1.0406541e+10 -0.54000141
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3700 0 1.0577151e+10 -0.54002354
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3800 0 1.0488249e+10 -0.53996003
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3900 0 1.0316153e+10 -0.54002024
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4000 0 1.0491289e+10 -0.5400259
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4100 0 1.0587981e+10 -0.5399811
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4200 0 1.0332035e+10 -0.53997951
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4300 0 1.0776469e+10 -0.53994151
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4400 0 1.0982142e+10 -0.53983842
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4500 0 1.0796919e+10 -0.5398414
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4600 0 1.0324249e+10 -0.53979712
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4700 0 1.0420899e+10 -0.53981967
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4800 0 1.0274188e+10 -0.53976759
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4900 0 1.0411535e+10 -0.5397757
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5000 0 1.0399215e+10 -0.53980199
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Loop time of 1.34285 on 1 procs for 5000 steps with 1024 atoms
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Performance: 0.032 tau/day, 3723.422 timesteps/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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Pair | 0.25309 | 0.25309 | 0.25309 | 0.0 | 18.85
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.068734 | 0.068734 | 0.068734 | 0.0 | 5.12
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Output | 0.0012887 | 0.0012887 | 0.0012887 | 0.0 | 0.10
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Modify | 0.96552 | 0.96552 | 0.96552 | 0.0 | 71.90
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Other | | 0.05422 | | | 4.04
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Nlocal: 1024.00 ave 1024 max 1024 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 201.000 ave 201 max 201 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2112.00 ave 2112 max 2112 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2112
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Ave neighs/atom = 2.0625000
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Neighbor list builds = 0
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Dangerous builds = 0
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reset_timestep 0
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# MSD
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compute msd all msd
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thermo_style custom step temp epair c_msd[*] c_press
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timestep 0.00001
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thermo 1000
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# main run
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run 20000
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Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes
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Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
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0 1.0409381e+10 0 0 0 0 0 -0.53980199
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1000 107022.73 0.0080050427 0.020451432 0.021388798 0 0.04184023 -0.54900967
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2000 107475.82 0.017262846 0.040669645 0.044251149 0 0.084920794 -0.42740968
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3000 105388.35 0.042257875 0.062828995 0.05845782 0 0.12128682 -0.31792184
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4000 106238.38 0.052733384 0.079036841 0.079396453 0 0.15843329 -0.24243699
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5000 102904.54 0.088524456 0.095977642 0.099533961 0 0.1955116 -0.093468615
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6000 105274.15 0.065334999 0.11591691 0.11675531 0 0.23267222 -0.21904478
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7000 108903.41 0.06724271 0.13694218 0.13914947 0 0.27609164 -0.15913012
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8000 101451.44 0.097201152 0.15704893 0.16178845 0 0.31883738 -0.055786965
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9000 106808.72 0.084301668 0.18029391 0.175753 0 0.3560469 0.014898739
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10000 107381.19 0.088583354 0.2000753 0.19569789 0 0.39577319 0.19417596
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11000 102105.78 0.081066654 0.22042599 0.21914042 0 0.43956641 0.060574143
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12000 105384.94 0.098716908 0.24382064 0.24673594 0 0.49055657 0.17067875
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13000 107479.53 0.099989043 0.26942088 0.27207566 0 0.54149654 0.25514896
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14000 102938.12 0.093252916 0.28529564 0.28698837 0 0.57228401 0.19976355
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15000 104408.02 0.11900926 0.31291315 0.31195058 0 0.62486373 0.36956014
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16000 103447.68 0.09627777 0.34145225 0.33159885 0 0.6730511 0.29857404
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17000 108400.05 0.11433561 0.36561966 0.36068301 0 0.72630267 0.41922801
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18000 103363.68 0.11040153 0.38709746 0.39228677 0 0.77938423 0.38111686
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19000 103310.43 0.10660536 0.41406235 0.40975085 0 0.8238132 0.36022184
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20000 102692.1 0.13517651 0.43870812 0.44138776 0 0.88009588 0.51144366
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Loop time of 5.66207 on 1 procs for 20000 steps with 1024 atoms
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Performance: 3051.889 tau/day, 3532.279 timesteps/s
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99.9% 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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Pair | 1.3123 | 1.3123 | 1.3123 | 0.0 | 23.18
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Neigh | 0.011856 | 0.011856 | 0.011856 | 0.0 | 0.21
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Comm | 0.2747 | 0.2747 | 0.2747 | 0.0 | 4.85
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Output | 0.0011516 | 0.0011516 | 0.0011516 | 0.0 | 0.02
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Modify | 3.8451 | 3.8451 | 3.8451 | 0.0 | 67.91
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Other | | 0.2169 | | | 3.83
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Nlocal: 1024.00 ave 1024 max 1024 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 184.000 ave 184 max 184 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2558.00 ave 2558 max 2558 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2558
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Ave neighs/atom = 2.4980469
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Neighbor list builds = 23
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Dangerous builds = 0
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Total wall time: 0:00:07
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