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new USER-MESO package

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Steve Plimpton
2017-08-18 17:33:42 -06:00
parent b11fe2eddb
commit f945d4567d
81 changed files with 8358 additions and 66 deletions
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examples/USER/meso/mdpd/in.mdpd Normal file
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########################################################################
#### 3D droplet oscilation using many-body DPD simulation ###
#### ###
#### Created : Zhen Li (zhen_li@brown.edu) ###
#### Division of Applied Mathematics, Brown University. ###
#### ###
#### mDPD parameters follow the choice of the publication: ###
#### Z. Li et al. "Three dimensional flow structures in a moving ###
#### droplet on substrate: a dissipative particle dynamics study" ###
#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
atom_style mdpd
region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd
lattice fcc 6
region film block -20 20 -7.5 7.5 -2.0 2.0 units box
create_atoms 1 region film
pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
pair_coeff 1 1 mdpd/rhosum 0.75
pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
mass 1 1.0
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 38497 loop local dist gaussian
fix mvv all mvv/dpd
#dump mydump all atom 100 atom.lammpstrj
#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 &
# view 90 90 box no 0 size 600 200
#dump_modify jpg pad 4
#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 &
# view 90 90 box no 0 size 600 200
#dump_modify avi pad 4
timestep 0.01
run 4000

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examples/USER/meso/mdpd/log.16Aug17.mdpd.g++.1 Normal file
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LAMMPS (11 Aug 2017)
########################################################################
#### 3D droplet oscilation using many-body DPD simulation ###
#### ###
#### Created : Zhen Li (zhen_li@brown.edu) ###
#### Division of Applied Mathematics, Brown University. ###
#### ###
#### mDPD parameters follow the choice of the publication: ###
#### Z. Li et al. "Three dimensional flow structures in a moving ###
#### droplet on substrate: a dissipative particle dynamics study" ###
#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
atom_style mdpd
region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd
Created orthogonal box = (-25 -10 -10) to (25 10 10)
1 by 1 by 1 MPI processor grid
lattice fcc 6
Lattice spacing in x,y,z = 0.87358 0.87358 0.87358
region film block -20 20 -7.5 7.5 -2.0 2.0 units box
create_atoms 1 region film
Created 14333 atoms
pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
pair_coeff 1 1 mdpd/rhosum 0.75
pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
mass 1 1.0
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 38497 loop local dist gaussian
fix mvv all mvv/dpd
dump mydump all atom 100 atom.lammpstrj
#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200
#dump_modify jpg pad 4
#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200
#dump_modify avi pad 4
timestep 0.01
run 4000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 77 31 31
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair mdpd/rhosum, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair mdpd, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.931 | 9.931 | 9.931 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -13.346542 0 -11.846647 -6.8495478
100 1.0321029 -7.2846779 0 -5.7366316 -0.77640205
200 1.042287 -6.9534532 0 -5.3901317 -0.27750815
300 1.0583027 -6.8483105 0 -5.2609672 -0.30347708
400 1.0493719 -6.8648608 0 -5.2909127 -0.15312495
500 1.0723786 -6.8341085 0 -5.2256528 0.017227511
600 1.0545695 -6.8152957 0 -5.2335517 -0.024362439
700 1.0507193 -6.8076033 0 -5.2316344 -0.07101536
800 1.0531856 -6.9378568 0 -5.3581886 -0.053943939
900 1.0442995 -6.8501126 0 -5.2837726 -0.13347942
1000 1.0335049 -6.8883554 0 -5.3382062 -0.18420426
1100 1.0287276 -6.8298226 0 -5.2868389 -0.12081558
1200 1.0322527 -6.9462828 0 -5.3980117 -0.18047625
1300 1.0599443 -6.9449975 0 -5.355192 -0.011763589
1400 1.0560932 -6.845479 0 -5.2614498 0.032130055
1500 1.0432786 -6.9035877 0 -5.338779 -0.10268662
1600 1.064183 -6.9116836 0 -5.3155205 -0.060722129
1700 1.0586249 -6.8768278 0 -5.2890013 0.037005566
1800 1.0576064 -7.0060193 0 -5.4197204 -0.036211254
1900 1.0595141 -6.838741 0 -5.2495807 -0.12395681
2000 1.0650509 -6.897976 0 -5.3005111 0.003594807
2100 1.0768273 -6.8874245 0 -5.2722962 0.033283489
2200 1.0511606 -6.9823162 0 -5.4056854 0.015008427
2300 1.0461138 -6.8820601 0 -5.3129988 0.064646933
2400 1.0485369 -6.9437148 0 -5.3710191 -0.16534939
2500 1.0507221 -6.9394786 0 -5.3635054 -0.098289859
2600 1.0518352 -6.8947578 0 -5.3171152 -0.011666785
2700 1.0402369 -6.9273377 0 -5.3670913 0.035267073
2800 1.0426109 -6.912024 0 -5.3482168 0.049597305
2900 1.0358928 -6.9574778 0 -5.4037471 -0.063216561
3000 1.0351023 -6.9844192 0 -5.4318742 -0.10323465
3100 1.0255005 -6.9382486 0 -5.4001052 -0.073954735
3200 1.0150616 -6.9843183 0 -5.4618321 -0.095136405
3300 1.0118112 -6.9522082 0 -5.4345973 -0.12686179
3400 1.0071522 -6.970158 0 -5.4595351 -0.012487475
3500 1.0041758 -6.9773019 0 -5.4711433 -0.098027653
3600 1.0189298 -6.9393039 0 -5.4110158 0.061631719
3700 1.012442 -6.9341423 0 -5.4155852 0.10442772
3800 1.0021246 -6.9594374 0 -5.4563553 -0.081535223
3900 1.0165002 -6.9045321 0 -5.3798882 -0.0088283303
4000 1.0077099 -6.9145511 0 -5.4030918 0.048349691
Loop time of 135.409 on 1 procs for 4000 steps with 14333 atoms
Performance: 25522.736 tau/day, 29.540 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 | 93.074 | 93.074 | 93.074 | 0.0 | 68.74
Neigh | 40.192 | 40.192 | 40.192 | 0.0 | 29.68
Comm | 0.19625 | 0.19625 | 0.19625 | 0.0 | 0.14
Output | 0.41756 | 0.41756 | 0.41756 | 0.0 | 0.31
Modify | 1.0706 | 1.0706 | 1.0706 | 0.0 | 0.79
Other | | 0.4581 | | | 0.34
Nlocal: 14333 ave 14333 max 14333 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11 ave 11 max 11 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 401803 ave 401803 max 401803 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 803606 ave 803606 max 803606 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 803606
Ave neighs/atom = 56.0668
Neighbor list builds = 1050
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:02:15

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LAMMPS (11 Aug 2017)
########################################################################
#### 3D droplet oscilation using many-body DPD simulation ###
#### ###
#### Created : Zhen Li (zhen_li@brown.edu) ###
#### Division of Applied Mathematics, Brown University. ###
#### ###
#### mDPD parameters follow the choice of the publication: ###
#### Z. Li et al. "Three dimensional flow structures in a moving ###
#### droplet on substrate: a dissipative particle dynamics study" ###
#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
atom_style mdpd
region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd
Created orthogonal box = (-25 -10 -10) to (25 10 10)
4 by 1 by 1 MPI processor grid
lattice fcc 6
Lattice spacing in x,y,z = 0.87358 0.87358 0.87358
region film block -20 20 -7.5 7.5 -2.0 2.0 units box
create_atoms 1 region film
Created 14333 atoms
pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
pair_coeff 1 1 mdpd/rhosum 0.75
pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
mass 1 1.0
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 38497 loop local dist gaussian
fix mvv all mvv/dpd
dump mydump all atom 100 atom.lammpstrj
#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200
#dump_modify jpg pad 4
#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200
#dump_modify avi pad 4
timestep 0.01
run 4000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 77 31 31
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair mdpd/rhosum, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair mdpd, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 6.265 | 6.655 | 7.045 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -13.346542 0 -11.846647 -6.9757225
100 1.0406108 -7.2500697 0 -5.6892624 -0.80306477
200 1.0535506 -6.9452928 0 -5.3650772 -0.39911584
300 1.0644295 -6.8599907 0 -5.2634577 -0.2997968
400 1.0780123 -6.9471342 0 -5.3302286 -0.06274869
500 1.0672153 -6.8269984 0 -5.2262872 0.021251762
600 1.0634304 -6.8366569 0 -5.2416226 -0.021863333
700 1.0544807 -6.8272074 0 -5.2455967 -0.0064688066
800 1.0556172 -6.8859788 0 -5.3026634 0.023983333
900 1.0436201 -6.9246523 0 -5.3593313 -0.12409618
1000 1.0617016 -6.8632331 0 -5.2707919 -0.1145505
1100 1.0323831 -6.951554 0 -5.4030874 -0.030031884
1200 1.0407785 -6.931048 0 -5.3699892 -0.018362136
1300 1.0380953 -6.8785296 0 -5.3214953 -0.099308737
1400 1.0418898 -6.8998 0 -5.3370743 -0.14199421
1500 1.0487254 -6.9671212 0 -5.3941429 -0.12132644
1600 1.0561042 -6.8948881 0 -5.3108424 -0.09627292
1700 1.0524479 -6.9531441 0 -5.3745823 -0.11959782
1800 1.0541197 -6.9219819 0 -5.3409126 0.032964029
1900 1.0531221 -6.8805815 0 -5.3010085 0.030124685
2000 1.0531819 -6.8612868 0 -5.2816242 -0.076876781
2100 1.0757791 -6.919875 0 -5.3063189 -0.04060439
2200 1.069423 -6.9005754 0 -5.2965527 0.015347467
2300 1.0403109 -6.9015402 0 -5.3411827 0.0034687897
2400 1.0547448 -6.9325539 0 -5.3505471 -0.021202325
2500 1.0404195 -6.8494675 0 -5.2889472 0.086947847
2600 1.0499828 -6.9861392 0 -5.4112749 -0.018079308
2700 1.0294278 -6.8525151 0 -5.3084811 0.16911472
2800 1.0220652 -6.8993978 0 -5.366407 0.064820531
2900 1.0347904 -6.9322703 0 -5.3801929 -0.11384964
3000 1.0391372 -6.9519088 0 -5.3933117 0.003050577
3100 1.0335828 -7.0090074 0 -5.4587413 -0.17366664
3200 1.0211896 -6.9421289 0 -5.4104513 0.025299853
3300 1.0019232 -6.9426488 0 -5.4398688 -0.098334724
3400 1.0203541 -6.9310981 0 -5.4006737 -0.0015544982
3500 1.0076794 -6.9519932 0 -5.4405796 -0.056956902
3600 1.0086525 -6.9620979 0 -5.4492247 0.020014884
3700 1.0046112 -7.0011625 0 -5.4943508 -0.083936527
3800 1.0096867 -6.9470382 0 -5.4326138 -0.089521759
3900 1.0074482 -6.9959414 0 -5.4848745 -0.11873698
4000 1.01222 -6.9535694 0 -5.4353454 0.042191466
Loop time of 63.0327 on 4 procs for 4000 steps with 14333 atoms
Performance: 54828.695 tau/day, 63.459 timesteps/s
98.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.591 | 29.795 | 42.814 | 236.6 | 47.27
Neigh | 2.0347 | 10.239 | 18.555 | 255.6 | 16.24
Comm | 0.70099 | 6.0601 | 11.386 | 207.4 | 9.61
Output | 0.20713 | 0.40902 | 0.61087 | 31.5 | 0.65
Modify | 0.058089 | 0.27033 | 0.4851 | 40.7 | 0.43
Other | | 16.26 | | | 25.79
Nlocal: 3583.25 ave 7207 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1055.75 ave 2131 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 100549 ave 202192 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 201098 ave 404372 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 804390
Ave neighs/atom = 56.1215
Neighbor list builds = 1049
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:03