LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a...
Transcript of LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a...
![Page 1: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/1.jpg)
Winmostar tutorialLAMMPS
Dissipative Particle Dynamics(DPD)V7.021
X-Ability Co,. Ltd.
2017/07/06
![Page 2: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/2.jpg)
Contents
Configure
I. Build a simulation cell
II. Potential setting
III. LAMMPS setting
IV. Execute simulations
V. Analyze
Appendix 1: Insert branches
Appendix 2: Convert to coordinates of classical MD
2017/07/06[
![Page 3: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/3.jpg)
ConfigureSet up LAMMPS and Cygwin in advance.
Set up LAMMPS by following LAMMPS Installation Guide located at https://winmostar.com/en/manual_en.html.
2017/07/06[
![Page 4: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/4.jpg)
Click MD | DPD | DPD Cell Builder.
2017/07/06[
I. Build a simulation cell
![Page 5: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/5.jpg)
I. Build a simulation cell
1. Click A in Monomers Available box, set # of Monomers to 3, then click Add.
2. Click B, set # of Monomers to 3, then click Add.
Click Add on
# of Monomers
2017/07/06[
![Page 6: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/6.jpg)
I. Build a simulation cell
Set # of Polymers to 1440. Click Add.
2017/07/06[
![Page 7: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/7.jpg)
I. Build a simulation cell1. Set Density to 5 (this unit has no dimension) , and click Build.
2. Click Close.
The simulation cell will
be displayed here.
2017/07/06[
![Page 8: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/8.jpg)
I. Build a simulation cell
For the visualization, click View | Pack into PBC cell | Atom.
Particles crossing periodic
boundaries are carried over
to the other side.
2017/07/06[
![Page 9: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/9.jpg)
II. Potential setting
Click MD | DPD | DPD potential editor.
2017/07/06[
![Page 10: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/10.jpg)
1. Click New to create a new potential file.
2. Set Enter name to groot, click OK.
II. Potential setting
2017/07/06[
![Page 11: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/11.jpg)
1. Click on Nonbond tab, click the row of A B 15.00 1.00.
2. Set the bottom textbox to 21, click Set.
(the unit of both Aij and Rcut has no dimension.)
There are several ways to determine Aij for any monomers.
For example, see Winmostar Gromacs tutorial “Solubility/χ/DPD Parameters”
II. Potential setting
2017/07/06[
![Page 12: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/12.jpg)
Click OK to Potential Editor.
II. Potential setting
2017/07/06[
![Page 13: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/13.jpg)
III. LAMMPS setting
Click MD | LAMMPS | Keywords Setup.
2017/07/06[
![Page 14: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/14.jpg)
III. LAMMPS setting
1. Set Units to LJ, Ensemble to nve, # of Time Steps to 50,000.
2. Click OK. (Temperature, pressure, and time parameters are dimensionless)
2017/07/06[
![Page 15: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/15.jpg)
III. LAMMPS setting
2017/07/06[
Set MPI processes in the Option tab as needed.
![Page 16: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/16.jpg)
IV. Execute simulations
Click MD | LAMMPS | Start LAMMPS.
Set File Name to DPD. Click Save.
2017/07/06[
![Page 17: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/17.jpg)
V. Analyze
Click MD | LAMMPS | Import Trajectory. Open the file by default.
Lamellar phase appears due
to microphase separation
2017/07/06[
![Page 18: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/18.jpg)
Click Start or End to insert branches.
[Start]:Branching begins from preceding
particle
[End]:Ends branching initiated by [Start]
Appendix1: Insert branches
e.g.: Star-shaped Polymer
e.g.: Comb-shaped polymer
2017/07/06[
![Page 19: LAMMPS Dissipative Particle Dynamics DPD - WinmostarDPD)V7.pdf · Contents Configure I. Build a simulation cell II. Potential setting III. LAMMPS setting IV. Execute simulations V.](https://reader034.fdocuments.in/reader034/viewer/2022050720/5ae2f7417f8b9a5d648d4e86/html5/thumbnails/19.jpg)
Appendix2:
Converting to classical MD coordinatesSee following instructions when converting coordinates of DPD to coordinates
of classical (all atoms) MD.
1. Click MD | Polymer | Map monomers.
2. Set the map of monomers to each particle in the Monomer field, input
Density, then click Build.
3. Register the monomer via MD | Polymer | Register Monomer
(See Winmostar LAMMPS tutorial: Polymer modeling)
Please note, conversion processing time depends on the number of particles.
2017/07/06[