Course Syllabus

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2016 Phys 8112:  Topics in Soft Matter Physics Theory and Modeling

Instructor: Yeng-Long Chen (yenglong@phys.sinica.edu.tw)

Time: Friday morning 9:10-12:10

Classroom: Physics Room 716

Class website: softphys.wordpress.com

Recommended Texts:  Intermolecular and Surface Forces – J. Israelachvili

Basic Concepts for Simple and Complex Liquids – J-L. Barrat and J.P. Hansen

Syllabus     

Week 1            2/26  Introduction to soft matter and computer modeling

Week 2            3/4  Introduction to statistical mechanics for soft matter physics

Week 3            3/11  Van der Waals forces in soft matter  + Electrostatic forces and Poisson Boltzmann theory in soft matter

Week 4            3/18 Electrostatic forces and Poisson Boltzmann theory in soft matter  + Entropy forces and DLVO theory of colloids

Week 5            3/25   Self assembly and phase transition of amphiphilic molecules, polymers, and liquid crystals

Week 6           4/8   Phase transitions :  Ising model, Landau theory, Self-consistent field theory.

Week 7           4/15  Midterm Exam

Week 8            4/22 Introductory polymer physics

Week 10          4/29   Introductory complex fluid dynamics

Week 11          5/6   Complex fluid dynamics

Week 12          5/13   Project Lab

Week 13          5/20   Project Lab

Week 14         5/27      Project Lab

Week 15          6/3    Project Lab

Week 16          6/4   Make Up Project Lab

Week 17          6/17  Project Lab

Week 18          Final

 

 Homework 1: 20 – Due 4/6

 Homework 2: 20 – Due 5/20

 Midterm exam:  20

 Final Exam + Project : 40

Project grading

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Project Report (20 pts) 

5 – 10 pages

Clearly define purpose and physics (8 pts)

Clearly define methods (5 pts)

Clearly discuss results and physical significance (7 pts)

 

04/08, 04/29 TA Session

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The 04/08 session is about using VMD to visualize and analyze simulation results, and the 04/29 session is about using LAMMPS to perform MD simulation.

4/08 slides – VMD

VMD

4/29 slides – LAMMPS

LAMMPS

 

The sample input script for LAMMPS and the corresponding data files are shown below:

A) in.poly

# Initialization
units real
boundary f f f
atom_style molecular
read_data data.poly

# Potential information
neighbor 5.0 bin
bond_style harmonic
bond_coeff 1 50 2.2
angle_style harmonic
angle_coeff 1 30 160
dihedral_style harmonic
dihedral_coeff 1 40.0 1 2
pair_style lj/cut 10.5
pair_coeff 1 1 0.112 4.01 10.5
#####################################################
# Equilibration (Langevin dynamics at 300 K)

velocity all create 300.0 1231
fix 1 all nve
fix 2 all langevin 300.0 300.0 100.0 904297
thermo_style custom step temp pe etotal epair ebond eangle edihed
thermo 5000
timestep 1

dump 1 all xyz 50 conformation.xyz

run 100000

B) data.poly

10 atoms
9 bonds
8 angles
7 dihedrals

1 atom types
1 bond types
1 angle types
1 dihedral types

-100.0 100.0 xlo xhi
-100.0 100.0 ylo yhi
-100.0 100.0 zlo zhi

Masses

1 14.02

Atoms

1 1 1 0 0 0
2 1 1 0 0 2
3 1 1 0 0 4
4 1 1 0 0 6
5 1 1 0 0 8
6 1 1 0 0 10
7 1 1 0 0 12
8 1 1 0 0 14
9 1 1 0 0 16
10 1 1 0 0 18

Bonds

1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
6 1 6 7
7 1 7 8
8 1 8 9
9 1 9 10
Angles

1 1 1 2 3
2 1 2 3 4
3 1 3 4 5
4 1 4 5 6
5 1 5 6 7
6 1 6 7 8
7 1 7 8 9
8 1 8 9 10
Dihedrals

1 1 1 2 3 4
2 1 2 3 4 5
3 1 3 4 5 6
4 1 4 5 6 7
5 1 5 6 7 8
6 1 6 7 8 9
7 1 7 8 9 10

Week 10 Intro to computations in soft matter physics

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Some ideas for the projectNotes Week 9 Phys – Introduction to computer modeling of

Week 9 – FrenkelSmit – Chapter 3 – Monte Carlo Method

Week 11 – FrenkelSmit – Chapter 6 – Molecular Dynamics in various ensembles

Week 11 – FrenkelSmit – Appendix E – Integration Schemes

Instructions for molecular dynamics

NTU-MDNP intro 2

Some ideas for the project

Week 10 – FrenkelSmit – Chapter 13 – Advanced MC moves