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Updated: 10 hours 22 min ago

Hi Bernard,

Wed, 2014-10-01 06:48

In reply to Hi Bernad,

Hi Bernard,

Well, I have already got my .odb, .fil, .dat  of my protein now  want to extract Eigenvector for each mode then compute the Protein B-factor.

Christian,

bope0001@e.ntu.edu.sg

Extract EigenVector for each mode 3Nx3N

Wed, 2014-10-01 05:03

In reply to Using Abaqus Student version for mollecular modeling (input file xx.pdb)

Any idea how to extract eigenvector for each mode in .odb file?
I have the Eigenvalue, Freq and generalized mass.
The problem is I need to extract the eigenvector (3Nx3N) which mean that the first 6 should be zero of all mode which will be use to calculate the Boltzman factor (B-Factor) for my protein.

Regards,

Christian

Hi Bernad,

Wed, 2014-10-01 04:55

In reply to Abaqus

Hi Bernad,

Sorry my late reply, in Abaqus I;m running Normal Mode Analysis for a protein.

christian

You can see which FEA

Wed, 2014-10-01 01:05

In reply to Heat transfer solver?

You can see which FEA products have at least some kind of heat transfer functionality on http://feacompare.com. It also indicates what kind of preprocessor it has. There's not a lot in the "free" price range that is both user-friendly and supports heat transfer solving.

 

Rotor Dynamics and Abaqus

Tue, 2014-09-30 13:08

In reply to In my opion, to the comples

Can you please suggest me a simple running problem in Abaqus..

My pleasure

Tue, 2014-09-30 04:11

In reply to Dear Prof. Bigoni,

Dear Dibakar Datta,

thank you for your nice comment!
I am really glad that you have enjoyed reading my book.

Davide

 

 

Dear Prof. Zhou,

Tue, 2014-09-30 00:03

In reply to boundary conditions and Flory-Huggins coefficient

Dear Prof. Zhou,

1. The mechanical boundary condition is traction-free because in the experiment the whole hybrid gel sheet is free-standing. But I guess maybe you were talking about how we impose temperature B.C.? We did not really control the temperature. Instead, we artificially assign a change of chemical potential to the hybrid sheet to mimic the volume change of BG and LG in response to temperature change. To ensure this is physical and realistic, we fine tune the chemical potential to make sure the size change of BG and LG in the simulation matches that measured in experiments (experimentally measured size change is shown in Fig.3)

2 No, we employed constant Flory-Huggins interaction coefficient. Because we did not really simulate the temperature-induced phase transformation, we just used chemical potential to control the volume change and thus mimic the deformation process of hybrid sheet, in that sense, we don't need temperature-dependent Chi

Best regards,

Dear Prof. Bigoni,

Mon, 2014-09-29 21:21

In reply to Torsional locomotion

Dear Prof. Bigoni,

I really enjoyed reading your book : Nonlinear Solid Mechanics: Bifurcation Theory and Material Instability. Your work is truly inspiring. 

Thank you.

boundary conditions and Flory-Huggins coefficient

Sun, 2014-09-28 22:46

In reply to Hybrid hydrogel sheets that undergo pre-programmed shape transformations

Dear Zheng,

Another two questions:

1. How did you enforce boundary conditions for the simulation in Figure 1? How did you know the boundary conditions is physical and realistic?

2. Did you use a temperature-dependent Flory-Huggins interaction coefficient? Have you fitted it to experiment?

Jinxiong

script for element connectivity

Sun, 2014-09-28 09:46

In reply to ABAQUS Element Connectivity

Hello

the code below will generate a file listing (in my example)

({'connectivity': (4980, 4981, 4982, 4983), 'instanceName': None, 'label': 1, 'type': C3D4}),4980

for all elements.
The 4 numbers are the nodes forming the element identified after 'label'
I do not recall what the last number stands for, it presumably repeats the first node number

Important: node numbers are shifted by one ! A node number 0 exists.
Check the output for a few elements by picking
ABAQUS/CAE : Tools-->Query-->Element

Good luck

Frank

----------------------------------------------------------------

import part

file = open('C:/Simulations/Shallow Notch/SN08/SN08-elements.txt','w+') # path and filename you want to generate

elemArr = mdb.models['Model-1'].parts['UFTE_SN_ohne_Gewinde'].elements # pick the part you want to analyse
len(elemArr)
# print elemArr
print len(elemArr)
#a = mdb.models['Model-1'].parts['Model-1']
#print a
#allNodes = a.nodes
#print allNodes
#rootAssembly
#elemente = a.elements[1]
# for e in elemArr:
  # print e.getNodes()
  # print e,' : ', e.connectivity
 
for e in elemArr:
    file.write('%s,%g\n' % (e, e.connectivity[0]))

file.close()

Thank you very much!

Sun, 2014-09-28 04:04

In reply to Thanks for your questions, Dear Prof. Zhou.

Dear Zheng, Thank you for your detailed answering. Jinxiong

Thanks for your questions, Dear Prof. Zhou.

Sun, 2014-09-28 03:43

In reply to Two questions

Dear Prof. Zhou, thank you so much for your interest in our work. I would like to first briefly introduce the storyline of our paper and I think it could help me to better answer your questions. Basically, we did simulations with various nominal densities of polymer chains (the parameter N) of BG and the results indicate that, by tuning N of BG, different deformation modes (1-4) can be achieved. The simulation results are summarized in Fig.1. Inspired by our simulation findings, our collaborators carried out experiments with different crosslinker densities of BG (because crosslinker density is closely related to N) to get those deformation modes predicted by simulations. Modes 1-3 are detected in the experiments. The experimental findings are summarized in Fig.2-5. Now, let's get back to your questions:

1. I am sure you know our model very well. In the simulations, we prescribed N directly and N carries information about the modulus of BG (since NkT is the initial shear modulus of the dry state). The conclusion of the simulation is: different N's lead to different deformation modes. But we did not quantitatively correlate N with concentration of BIS crosslinker (shown in Fig. 4) because we do not have enough experimental measurements to correlate them. However, this does not affect the storyline of this paper.

2. You are absolutely right, our simulation is for equilibrium state. However, the time dependent data in Fig.3 was measured from experiments, not simulations. We just used simulation plots (intermediate states before the final equilibrium solution is reached) as illustration to schematically show how the hybrid sheet looks like for each data point in Fig.3. We did this because 1) for each data point, we compared the simulated intermediate shape with the real shape experimentally observed and they look quite similar. 2) the simulation plot has better qualities than the experimental photos in which gels are translucent. Therefore, those plots are used as illustration and they are not necessary to carry real physical meanings.

 

Please kindly let me know if these answer your questions. Please don't hesitate to contact me if you would like to discuss more. Many thanks!

 

Two questions

Sat, 2014-09-27 21:32

In reply to Hybrid hydrogel sheets that undergo pre-programmed shape transformations

Dear Zheng,

Thanks for sharing this very interesting paper, which is really an excellent work. I just take a glance and have two quick questions. 

1. The elastic modulus of BG depends on the concentration of crosslinker BIG as indicated in Fig. 4 of your paper. In your simulation model, how did you incorporate the variation of modulus with concentration of BIG?

2. I guess your simulation is an equilibrium state simulation, so you do not have time. In Fig3 (b) you show the time depedent width of BG or LG. How can you obtain this?

Thanks. 

Jinxiong

Good Job ! congratulations !

Sat, 2014-09-27 16:30

In reply to Stretchability and compliance of freestanding serpentine-shaped ribbons

Good Job ! congratulations !

gurson

Sat, 2014-09-27 08:28

In reply to Ductile Failure using Gurson model Abaqus: Implicit and Explicit

Hello Khalid,

 

I do not have an answer your question. I am actually asking for your help.

I am going to use gurson model in abaqus. I do not know how would I do it !

Could you recommend reading materials , examples & tutorials ?

 

i appreciate your help.

Best,

Ahmed

Hello Khalid,

Sat, 2014-09-27 08:28

In reply to Ductile Failure using Gurson model Abaqus: Implicit and Explicit

Hello Khalid,

 

I do not have an answer your question. I am actually asking for your help.

I am going to use gurson model in abaqus. I do not know how would I do it !

Could you recommend reading materials , examples & tutorials ?

 

i appreciate your help.

Best,

Ahmed

Drucker pragger

Fri, 2014-09-26 05:18

In reply to Drucker Prager plasticity model for ceramics

I am PhD student at Italy. I would like to apply drucker pragger criterion for ceramic material at micro scale level and to implement this method in abaqus I trying to find plastic properties such as yield stress , internal friction  and cohession from lietrature but unfortunately there is no much information about plastic properties of this materials. I request any knows how to find the plastic properties of cermaic kindly let me know. Also, I need to know how to modify the DP criteriaon for multiaxial loading case.

strength of materials

Thu, 2014-09-25 04:24

In reply to Lecture notes of interest to mechanicians

while calculating shear stresses in beams,what is the meaning of average shear stree?

Re: Rate-dependent plasticity

Thu, 2014-09-25 00:34

In reply to Rate-independent plasticity vs viscous flow

Dear Zhigang, Figure 8 from our paper will give you a taste of the unusual behavior observed in aluminum alloys.

-- Biswajit

These are a number of research papers and textbooks

Wed, 2014-09-24 18:28

In reply to These are a number of research

 Submitted by ponjenku on Sun, 2013-09-01 05:54.

yes, These are a number of research papers and textbooks by Prof. W. Noll. I suppose they definitely deserve to be here.

Asus zenfone smartphone android terbaik

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