diff --git a/examples/USER/meso/edpd/in.edpd b/examples/USER/meso/edpd/in.edpd index 316099bce35ceb0f7e7fd370cf0862fd8c433804..af1a79d73daec55199bb3a5b835762a279e0b286 100644 --- a/examples/USER/meso/edpd/in.edpd +++ b/examples/USER/meso/edpd/in.edpd @@ -1,54 +1,54 @@ -######################################################################## -### Heat conduction analog of periodic Poiseuille flow problem ### -### using energy-conserving DPD (eDPD) simulation ### -### ### -### Created : Zhen Li (zhen_li@brown.edu) ### -### Division of Applied Mathematics, Brown University. ### -### ### -### mDPD system setup follows Fig.12 in the publication: ### -### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### -### "Energy-conserving dissipative particle dynamics with ### -### temperature-dependent properties". J. Comput. Phys., ### -### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### -######################################################################## -units lj -dimension 3 -boundary p p p -neighbor 0.2 bin -neigh_modify every 1 delay 0 check yes - -atom_style edpd - -region edpd block -10 10 -10 10 -5 5 units box -create_box 1 edpd -create_atoms 1 random 16000 276438 NULL -mass 1 1.0 -set atom * edpd/temp 1.0 -set atom * edpd/cv 1.0E5 - -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 1.41E-5 2.0 1.58 & - power 10.54 -3.66 3.44 -4.10 & - kappa -0.44 -3.21 5.04 0.00 - -compute mythermo all temp -thermo 100 -thermo_modify temp mythermo -thermo_modify flush yes - -velocity all create 1.0 432982 loop local dist gaussian - -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 lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 - -timestep 0.01 -run 500 -reset_timestep 0 - -compute temp all edpd/temp/atom -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 - -run 500 +######################################################################## +### Heat conduction analog of periodic Poiseuille flow problem ### +### using energy-conserving DPD (eDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### mDPD system setup follows Fig.12 in the publication: ### +### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### +### "Energy-conserving dissipative particle dynamics with ### +### temperature-dependent properties". J. Comput. Phys., ### +### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style edpd + +region edpd block -10 10 -10 10 -5 5 units box +create_box 1 edpd +create_atoms 1 random 16000 276438 NULL +mass 1 1.0 +set atom * edpd/temp 1.0 +set atom * edpd/cv 1.0E5 + +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 1.41E-5 2.0 1.58 & + power 10.54 -3.66 3.44 -4.10 & + kappa -0.44 -3.21 5.04 0.00 + +compute mythermo all temp +thermo 100 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +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 lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 + +timestep 0.01 +run 500 +reset_timestep 0 + +compute temp all edpd/temp/atom +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 + +run 500 diff --git a/examples/USER/meso/mdpd/in.mdpd b/examples/USER/meso/mdpd/in.mdpd index 201b4a340eefd272a3e0e8515a9301b26c9cb769..b0740c822767a59dfa38faacce9cc3c072b1a78d 100644 --- a/examples/USER/meso/mdpd/in.mdpd +++ b/examples/USER/meso/mdpd/in.mdpd @@ -1,52 +1,52 @@ -######################################################################## -#### 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 +######################################################################## +#### 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 diff --git a/examples/USER/meso/tdpd/in.tdpd b/examples/USER/meso/tdpd/in.tdpd index 748a4f50775795c51a26eead61adfaa3a6085477..5107e7a454256a52f2b4b6aed736556775a1e32a 100644 --- a/examples/USER/meso/tdpd/in.tdpd +++ b/examples/USER/meso/tdpd/in.tdpd @@ -1,54 +1,54 @@ -######################################################################## -### Pure diffusion with a reaction source term analog of a periodic ### -### Poiseuille flow problem using transport DPD (tDPD) simulation ### -### ### -### Created : Zhen Li (zhen_li@brown.edu) ### -### Division of Applied Mathematics, Brown University. ### -### ### -### tDPD system setup follows Fig.1 in the publication: ### -### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### -### "Transport dissipative particle dynamics model for mesoscopic ### -### advection-diffusion-reaction problems. J. Chem. Phys., ### -### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### -######################################################################## -units lj -dimension 3 -boundary p p p -neighbor 0.2 bin -neigh_modify every 1 delay 0 check yes - -atom_style tdpd 2 - -region tdpd block -10 10 -10 10 -5 5 units box -create_box 1 tdpd -create_atoms 1 random 16000 276438 NULL -mass 1 1.0 -set atom * cc 1 1.0 -set atom * cc 2 1.0 - -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 - -compute mythermo all temp -thermo 50 -thermo_modify temp mythermo -thermo_modify flush yes - -velocity all create 1.0 432982 loop local dist gaussian - -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 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 lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 - -timestep 0.01 -run 500 -reset_timestep 0 - -compute cc1 all tdpd/cc/atom 1 -compute cc2 all tdpd/cc/atom 2 -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 - -run 100 +######################################################################## +### Pure diffusion with a reaction source term analog of a periodic ### +### Poiseuille flow problem using transport DPD (tDPD) simulation ### +### ### +### Created : Zhen Li (zhen_li@brown.edu) ### +### Division of Applied Mathematics, Brown University. ### +### ### +### tDPD system setup follows Fig.1 in the publication: ### +### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### +### "Transport dissipative particle dynamics model for mesoscopic ### +### advection-diffusion-reaction problems. J. Chem. Phys., ### +### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### +######################################################################## +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes + +atom_style tdpd 2 + +region tdpd block -10 10 -10 10 -5 5 units box +create_box 1 tdpd +create_atoms 1 random 16000 276438 NULL +mass 1 1.0 +set atom * cc 1 1.0 +set atom * cc 2 1.0 + +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 + +compute mythermo all temp +thermo 50 +thermo_modify temp mythermo +thermo_modify flush yes + +velocity all create 1.0 432982 loop local dist gaussian + +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 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 lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 + +timestep 0.01 +run 500 +reset_timestep 0 + +compute cc1 all tdpd/cc/atom 1 +compute cc2 all tdpd/cc/atom 2 +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 + +run 100