Monday, January 14th, 2019: I met professor and set up the config together. There should be 4 simulations for OBSTACLE:2 (sphere).


Beginning my capstone, after summer break. Following are the setup conditions from Professor:

Bulk simulation with particle

Shape of the particle, OBSTACLE =1,2, 3 sphere and cube

rcut=1.112, rcut =2.5


Size of the particle with the same molecule (changes volume fraction)

Size ratio of molecule and particle,



Flow induced crystallization


1st simulation
i built start mode with 100,000 steplimit.
and equilibriate with, bodyforce=0.0
but not activate stress_bin
However when i showed the result to Prof. he said it’s good
previous sim, i put it in DUMP

2nd simulation
i rebuilt the start mode with only 5000 steplimit
turns out, out2 file has the same
then i activate stress_bin during equilibrate
I name it TASK2…rev in the PC folder
however keep the name TAG the same in winSCP

[TASK 4]
11 oct
After edited by Prof on the grid number, the START was run well
However i use steplimit 100000

12 oct
I edit the steplimit to 5000 in TASK4_start_rev
and successfuly built initial out2

Use it to Equilibrate
However stop at step mol 23??

seems that because of the StepGridZero 100,000 is too big given Step Equil is 10,000.

simulation 3, change stepgridzero to 5000–>stopped
simulation 4, stepgridzero 10000, StepEquil 20,000 –>stopped

sim 5, without grid activate, stress_bin=0, StepGridzero 100,000
coz I don’t care…LoL

step_webMoll stop at 91

13oct rerun but still stop at 91
change proc file

i use the out2 from 13oct (with step moll 91)
it works for g04, but i can’t open the grid file

change 8 but stopped

14 OKT
Running use more coarse grid

It worked for the g08, achieve stepwebmoll 100
grid file seems ok

I run equilibrium with coarse grid, just to check whether it will achieve moll 100, however i presume it wont be different coz the stress bin is not activated….and it achieve 100

then i use out2_equilibrate_coarse to run
next body force

TASK 2 – 18 Okt
at tutorial, checking progress with professor.
Able to do averaging and SI conversion
next to find steady state, find the velocity, Reynold number and the flow rate

TASK 2 – 19 OKT
Try to run the shorter timesteps
200,000 timesteps
stepGridZero i set to 20,000

I’ll put my logbook of the Computational USYD here. Just to keep it well documented and traceable. Artemis is a Supercomputer facility in USYD by which I do my simulation of Computational Nanotechnology.

Artemis login

Konten ini diproteksi dengan password. Untuk melihatnya cukup masukkan password Anda di bawah ini:

Semester 1, ga kemana-mana. Masih sekitar Sydney, eh kampus-rumah.


  1. Parramatta
  2. Blacktown
  3. Bankstown
  4. Newton
  5. Opera House
  6. Lakemba
  7. Maroubra

This post will sum up all of my impression and experiences I had during my first month of staying in Sydney. Well, actually it has been 1,5 months. Just to make it simple let’s call it a month. I’ll categorize them to make it more organized and easier to follow.

  1. Transportation. Even though it’s not as advanced as in Japan, the service is quite good and reliable. Means of transportation I used for daily commuting is train and bus. Other than that, New South Wales has LRT and wharf. The trip information can be accessed real time using some app. One of them is the Tripview. We can select the starting and the end position and the schedules so we can arrange and estimate our commuting time. It’s a handy app, so we can use our time better.
  2. Education. The education system, the method of learning and the resources are amazing. Student always being encouraged to have critical thinking. The academic culture in the uni is very high. Plagiarism is strongly avoided. One interesting event I had was the orientation week or O week-they usually called it. It’s one week before the commencement of a new semester. There were Welcoming sessions, faculty orientation, Library tour and the most exciting was the booth and exhibition from student clubs and student union. A lot of freebies and interesting events. What I found it best is that during the orientation, students were being prepared and introduced to uni life so that they can comfortably adjust to the new semester. Some of them are; library tour, get to know the library facilities and how to use the resources effectively. Faculty orientation provides an opportunity to get a more detailed look at the study. Even the director of the study spares their time to talk and gave one-on-one advice to the newcomers.
  3. Economy
  4. Way of life

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