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Commit a6eb5214 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
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strip off unwanted ^M characters

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examples/USER/meso/edpd/in.edpd
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######################################################################## ########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ### ### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ### ### using energy-conserving DPD (eDPD) simulation ###
### ### ### ###
### Created : Zhen Li (zhen_li@brown.edu) ### ### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ### ### Division of Applied Mathematics, Brown University. ###
### ### ### ###
### mDPD system setup follows Fig.12 in the publication: ### ### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### ### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ### ### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ### ### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### ### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
######################################################################## ########################################################################
units lj units lj
dimension 3 dimension 3
boundary p p p boundary p p p
neighbor 0.2 bin neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes neigh_modify every 1 delay 0 check yes
atom_style edpd atom_style edpd
region edpd block -10 10 -10 10 -5 5 units box region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd create_box 1 edpd
create_atoms 1 random 16000 276438 NULL create_atoms 1 random 16000 276438 NULL
mass 1 1.0 mass 1 1.0
set atom * edpd/temp 1.0 set atom * edpd/temp 1.0
set atom * edpd/cv 1.0E5 set atom * edpd/cv 1.0E5
pair_style edpd 1.58 9872598 pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58 #pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 & 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 & power 10.54 -3.66 3.44 -4.10 &
kappa -0.44 -3.21 5.04 0.00 kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp compute mythermo all temp
thermo 100 thermo 100
thermo_modify temp mythermo thermo_modify temp mythermo
thermo_modify flush yes thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/edpd 0.5 fix mvv all mvv/edpd 0.5
fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
timestep 0.01 timestep 0.01
run 500 run 500
reset_timestep 0 reset_timestep 0
compute temp all edpd/temp/atom compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0 compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500 run 500
examples/USER/meso/mdpd/in.mdpd
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######################################################################## ########################################################################
#### 3D droplet oscilation using many-body DPD simulation ### #### 3D droplet oscilation using many-body DPD simulation ###
#### ### #### ###
#### Created : Zhen Li (zhen_li@brown.edu) ### #### Created : Zhen Li (zhen_li@brown.edu) ###
#### Division of Applied Mathematics, Brown University. ### #### Division of Applied Mathematics, Brown University. ###
#### ### #### ###
#### mDPD parameters follow the choice of the publication: ### #### mDPD parameters follow the choice of the publication: ###
#### Z. Li et al. "Three dimensional flow structures in a moving ### #### Z. Li et al. "Three dimensional flow structures in a moving ###
#### droplet on substrate: a dissipative particle dynamics study" ### #### droplet on substrate: a dissipative particle dynamics study" ###
#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ### #### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
######################################################################## ########################################################################
units lj units lj
dimension 3 dimension 3
boundary p p p boundary p p p
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes neigh_modify every 1 delay 0 check yes
atom_style mdpd atom_style mdpd
region mdpd block -25 25 -10 10 -10 10 units box region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd create_box 1 mdpd
lattice fcc 6 lattice fcc 6
region film block -20 20 -7.5 7.5 -2.0 2.0 units box region film block -20 20 -7.5 7.5 -2.0 2.0 units box
create_atoms 1 region film create_atoms 1 region film
pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598 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/rhosum 0.75
pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75 pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
mass 1 1.0 mass 1 1.0
compute mythermo all temp compute mythermo all temp
thermo 100 thermo 100
thermo_modify temp mythermo thermo_modify temp mythermo
thermo_modify flush yes thermo_modify flush yes
velocity all create 1.0 38497 loop local dist gaussian velocity all create 1.0 38497 loop local dist gaussian
fix mvv all mvv/dpd fix mvv all mvv/dpd
#dump mydump all atom 100 atom.lammpstrj #dump mydump all atom 100 atom.lammpstrj
#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 & #dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 &
# view 90 90 box no 0 size 600 200 # view 90 90 box no 0 size 600 200
#dump_modify jpg pad 4 #dump_modify jpg pad 4
#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 & #dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 &
# view 90 90 box no 0 size 600 200 # view 90 90 box no 0 size 600 200
#dump_modify avi pad 4 #dump_modify avi pad 4
timestep 0.01 timestep 0.01
run 4000 run 4000
examples/USER/meso/tdpd/in.tdpd
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######################################################################## ########################################################################
### Pure diffusion with a reaction source term analog of a periodic ### ### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ### ### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ### ### ###
### Created : Zhen Li (zhen_li@brown.edu) ### ### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ### ### Division of Applied Mathematics, Brown University. ###
### ### ### ###
### tDPD system setup follows Fig.1 in the publication: ### ### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### ### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ### ### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ### ### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### ### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
######################################################################## ########################################################################
units lj units lj
dimension 3 dimension 3
boundary p p p boundary p p p
neighbor 0.2 bin neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes neigh_modify every 1 delay 0 check yes
atom_style tdpd 2 atom_style tdpd 2
region tdpd block -10 10 -10 10 -5 5 units box region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd create_box 1 tdpd
create_atoms 1 random 16000 276438 NULL create_atoms 1 random 16000 276438 NULL
mass 1 1.0 mass 1 1.0
set atom * cc 1 1.0 set atom * cc 1 1.0
set atom * cc 2 1.0 set atom * cc 2 1.0
pair_style tdpd 1.0 1.58 9872598 pair_style tdpd 1.0 1.58 9872598
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 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
compute mythermo all temp compute mythermo all temp
thermo 50 thermo 50
thermo_modify temp mythermo thermo_modify temp mythermo
thermo_modify flush yes thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/tdpd 0.5 fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01 fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
timestep 0.01 timestep 0.01
run 500 run 500
reset_timestep 0 reset_timestep 0
compute cc1 all tdpd/cc/atom 1 compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2 compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0 compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100 run 100
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